In case of the redesigned
Enterprise, I can simply look at
this cross-section or this
cross-section in order to see exactly what the designer intended with decks and windows. There are no doubt a couple of inconsistencies in the canon, but nobody will dispute the overall layout, because nobody disputes the intended size of a thousand feet, more or less. The entire subtle design, with all those windows and exterior hatches, would break down if that happened. This is what I mean by an explicit layout.
In case of the
Defiant, I can probably contact Tony Meininger who built the model in order to find out exactly what was intended for those lights, and yes, I might learn that they were supposed to be windows representing two decks, but that wouldn't matter. The 560' size was in dispute, Doug Drexler says he was asked to draw four decks, and so we ended up with a new layout of a 120m or so, one that remained in the canon.
Faced with such a contradiction (again, assuming I can prove those lights were supposed to be windows), I'm giving precedence to the canonical layout which tells me exactly what is supposed to be in that area, rather than the exterior which merely suggests what might be there. The rows of lights do have more canon appearances than the MSD, but since we don't know what they are, we give precedence to the exact schematics telling us how the ship is structured (the MSD and the derived deck plans).
In case of the
Valiant, you did see a window but you can't prove where it is supposed to be located, because there is no VFX shot matching the interior to the exterior (sort of like the final shot of the series). The
Defiant has all kinds of features behind hatches, so it is quite conceivable that the window is normally covered. If you take a look at screencap number 409 on
this page, you will see the plans for Decks 1-3. Screencap number 567 on
this page shows the Deck 4 plan.
Yes, "that thing" is the Type-10 shuttle (DS9TM nomenclature), and yes it was designed
along with the DS9TM schematics (OK, I'm not sure if it was precisely before or after the deck plans, but clearly around the time when those diagrams were drawn -- Doug Drexler mentions the interior cutaway). Drexler developed the shuttle and its bay, then sent over schematics for use on the show, and the same designs also ended up in the DS9 tech manual, released months later. The
Defiant's shuttle is named
Chaffee, and you probably saw it estimated at 9 meters because of its size in the DS9TM (9.64m), which is proportionally inconsistent with the stated width and height in the same book, and also with the scale of the shuttle in the deck plans (about 7m).
I asked Rick Sternbach about this, since he wrote the text, but he doesn't recall how he came up with that number -- my guess is he was measuring the Deck 3 plan using the assumed length of 171m. I also asked Brandon MacDougall who worked on that sequence at Foundation Imaging, but his model is 42 feet long and it was scaled down 15% from this size in order to fit the shot. (This number would make a lot of sense if the LightWave
Defiant was scaled at 560 feet in that shot, which we know was the preferred VFX size used in the CG model and by Gary Hutzel in general, but it wouldn't make any sense with Doug Drexler's design of the bay, so I'm treating it as a shot-specific outlier.)
Likewise, I asked Doug Drexler on his blog, and he said his copy of the LightWave model measures 26 feet. Larry Nemecek also posted a handwritten scale chart showing a 25' length, recorded during a meeting with Gary Hutzel. Based on this information, Doug Drexler's copy of the LightWave model is probably showing the intended scale, which was likely driven by Drexler's design of the interior bay, but it's hard to be sure, since no detailed exterior or interior sets were ever built.