Yes. It is there in 1960's photos, 1990's photos, and 2015/16 photos. And it is right where the drawings show it should be. It just isn't as obvious as the drawings have it.
The bulge can't really be spotted from a side profile. It's more obvious (but still subtle) if you are looking at a high res image of the 11' model from the front or rear angle to the side and compare the windows/pennant to a non-bulged shape.
If the bridge turns, moving up and down the process, it can solve a lot of issues about the offset. It does open up a debate about whether the "tall" position is for the bridge facing forward or offset by any amount. Regarding the vertical shafts in Jefferies diagram, while the one in the saucer seems to be intended to be a turbolift, I could see some of the others as conduits for the engine power, including horizontally, even though those are divided by bulkheads; I like the idea that the deflector, secondary hull engine room(s?) and nacelles are all connected to basically more-or-less one power conduit.
You can't see it in the side profile at all. You can only see it when looking at the secondary hull profile from an angle. The neck and the recesses disguise it and make it impossible to see from those angles. But when I was doing my drawings things just weren't coming out right in those areas until I added that in. The shape of the side indents (starboard and bottom) would not work out right until I added that additional detail. You could say all the time I spent on the Excelsior paid off in finding that missing detail. A lot of the oddities of these models are where during construction or during production use things didn't come out right. Excelsior and the TOS Enterprise have some interesting flaws, especially on the bottom of the saucer, where the shape is not quite perfect. Those imperfections are not reflected in my drawings. The TOS Enterprise also has an internal melt spot on the bow where the model was evidently tilted when that bow light was hot and it fell against the top of the saucer and created a small bulge. From all reports this was before it arrived at the Smithsonian. That isn't shown either.
While an interesting idea, it isn't very practical. I just go with the ship being refit and the production using outdated FX shots. This is a frequent thing during production during that time where they are not consistent with the vehicle or version of vehicle shown. I can't tell you how many time they used the wrong plane landing compared to the shots of the interior or of it flying. And WWII movies were really bad at that. So it is a product of the time TOS was made more than an indicator of a function of the ship. I am going by what I think Jefferies settled on and what the production documents had to say and what they continued on with in TMP. No no moving bridge, no retractable spikes. It was an earlier refit of the Enterprise and just a recycled shot used out of place. From The Corbomite Manuever on (first episode of season 1 produced), the bridge was short and the nacelles domes were spikeless and lit and the deflector was small.
I have a strong preference for basing decisions on what's on screen, only because that's probably the strongest level of evidence. That said, I think your solution is the most practical re: SFX.
Fact: SFX, set changes and script errors occurred in TOS. We just need to be smart enough to recognize them when they occur, then logically "fix" them using our imagination. So far as I can see, no two people on this site has identified all of them nor logically fixed them all the same. At least the same CGI Enterprise model was used for the remaster even though they didn't fix all the issues correctly.
I have not examined the CG Enterprise from the remastered version in great detail. It differs in window placement from the 11 foot model. Otherwise it is based on the 11 foot model. I'm not sure what relation the remastered CG model has to the Defiant CG model from Enterprise. The Defiant's windows seem closer, but it is based on the 1991 redress of the 11 foot model and features that same grid line design for the secondary hull and nacelles. It also features a different grid line pattern on the saucer (29 segments instead of 28). But that one does have phaser details on the hull. I personally ignore the remastered in terms of examining the ship (other than it was nicely consistent in which version, The Cage, WHMHGB, and Series).
Are any of these imperfections visible in an episode? There are things I see on the NASM version that aren't visible or present in the aired episodes.
I haven't noticed much in the episodes. I know you can see the wiring in a few episodes and the missing box, trench on the port side in at least one FX shot. but the surface imperfections really require stills at the right angles and in the FX shots in the episodes the ship is in constant motion which hides these imperfections. So I can't tell whether any of them are construction defects or defects that have appeared with age. The damage to the TOS saucer is obviously from use so it isn't a construction defect and none of the FX shots are from the right angle or high enough detail to capture it.
After looking at some screenshots, I had a very hard time seeing the additional phaser details on the CGI NCC-1764. I saw what looked like to blue details similar to ball turrets on the lower part of the saucer but nothing else new. If that was trying to look like the Franz Joseph phaser locations it is hard to tell.
They are all there in just a few frames. You can't really see the aft phasers until the beams cut off. Then they are visible for a few frames before the shot changes. And right after that there are just a couple still fames showing the forward phasers. They are just small emitters, not balls. I'm looking at 42:49 in Part II at the forward phasers. In that frame you can also see how the grid is off because the lower starboard registry is between two lines instead of on a line.
Yes, but you can't see it in the drawings. I need to make some construction drawings with the full turning profile of the secondary hull.
My favorite secondary hull was from Adias Sofia's Balson stretched the refit cigar to make it more teardrop shaped: http://www.shipschematics.net/startrek/images/federation/commandcruiser_balson.jpg I tried to widen the saucer of the refit a bit to match that secondary hull: https://www.trekbbs.com/threads/publiusrs-starship-designs-large-images.260404/
The question of what should be in the secondary hull comes to mind. An important question to ask is--What should the proportion of working space, cargo space, recreational space, and crew quarters be? Assuming that ships like the Saladin, with a crew of around 200 did exist, then would work/cargo areas found in the saucer be filled with crew quarters instead, to accommodate the larger crew on a Constitution? Or would the extra crew quarters be found in the secondary hull along with all the extra recreational facilities that apparently exist? The recreation area seen in TMP would likely have to be omitted on a refit-Saladin, if there were such a thing. In reality it would probably be a mix of the two. But the more I think about, the more that it seems that this would make each saucer much more of a custom job, which may or may not be desirable. On the other hand, it also seems odd that an engineering hull, supposed to give more power and a larger deflector, would also be full of recreation and crew facilities. In any case, all this seems to be a good argument for there being at least two engine rooms that look the one in TOS: one for the saucer that would be the only one on ships like the Saladin, Ptolemy and others, and at least one in the secondary hull for whatever increased power is down there. I think it is an idea worth considering that the secondary hull has two engine rooms: one with the pipe structure facing rear to the nacelles, and the other facing forward with the pipe structure going to the deflector, with the raised Emergency Manual monitor between them. In TOS we see characters working there and see one engine room behind them, but there would be another one in front of them, where the camera usually is. I'm not sure that she show ever showed the wall opposite the ladder in TOS, though at least one game shows it and prevents this notion, albeit only with a heavily modified ship.
The very open secondary hull of the refit made it look quite hollow. It could contain quite a few containers, but I’d like to think that was just a temporary affair… the incomplete TMP’s first trip to move medicine or perishables before extra decks were fitted. In ST-V we did finally see the shuttlebay get a back wall, though that was the dash-A
I consider the ST-V version to be more like the TOS would have been. It was built that way. The hollowness of the TMP version is because that hole is where the engine room used to be. So any Constitution Class that is refit would at least start that way, but might be finished off like the ST-V 1701-A.
I'm including 2 engine rooms. The season 1 engine room would have to be a little smaller than the set to fit within the confines of the hull at the back of the saucer. The season 2/3 Engine room is the real Warp Engine control room on the hanger deck in the secondary hull. The pipe structure sits between the engine room and the hanger area and is more in the middle of the secondary hull rather than pushed back toward the hanger and pylons. The plumbing to the pylons passes over any part of the hanger area that is forward of the hanger bulkhead. This allows the entry seen in Journey to Bable to be forward and the view into the hanger would be of the inside of the clamshell doors (there are no details on the far wall so it could literally be any of the walls in the hanger, but the inside of the doors is the most logical to be so featureless). I see no need for a 2nd pipe structure in the secondary hull so I have not included one. I consider the pipe structures to be the main energizers (which use dilithium to convert the warp core plasma into energy the ship can use). The saucer energizer provides power to the saucer and main weapons and shields while the secondary hull one provides power to the deflector, aft weapons, and the warp drive system. Auxilliary power is located in the saucer.