I am surprised you thought your weapons section would be controversial - the only thing I found myself disagreeing with was the notion that there are internal hull segments on ships with old-style "ball turrets." Does that mean you think there's an array under the hull? If so, why not just have ball turrets built with newer tech? I do agree with your assertion about why arrays are better and the role hull structure has to play in it.
My assumption with the refitted arrays is that the arrays are there under the hull, but only consist of the EPS conduit and prefire chamber. Basically they serve as very long "chambers" or "drums" for the emitter segment installed in the old spots where the ball turrets used to have their full equipment.
One reason was component commonality. Making a whole new set of parts and R&D design for non-arrayed emitters seems pretty wasteful.
Second, I figured the whole system was substantially more capable than the old one. So that even if you fed advances into the old configuration, you simply wouldn't get much out of it. So instead they use a common system and use the existing hull shape to do what the new arrays can do. That still comes with trade-offs, like the whole heat and fire arc issue, but it lets you use the same type of firepower between fleet common ships.
Also, when we start seeing the old 23rd century designs firing in DS9, they seem to only fire from one or two banks at any one time. That would make sense if they were tied together in some way and therefore could direct their energy in one or two banks rather than having to fire them all at once.
The other possibility is that making an old style emitter with comparable capacity as the arrays would require such a huge power cell or support machinery within the hull that it would make for a terrible technological upgrade. Pulse phasers being a minor exception, but even then those things are big suckers and have limited fire arcs.
In general having more "prefire chambers" scattered underneath the hull connected array segments is also partly an explanation why newer ships also seem to have array segments that are sub-divided along their hulls. So some of these arrays are actually parts of a larger array that's connected under the hull, but protected at the most vulnerable sections or emitter facets are removed to add some redundancy.