That makes sense now about why the blue was toned down. Would that be a huge oversight on ILM's part, seeing as they were heavily involved in the design? After all their experience with the Star Wars trilogy, and the troubles they had with bluescreening the enterprise in TWOK with its reflective paint, I would think Steve Gawley and Bill George would have been PAINFULLY aware of the problems with bluespill and would have taken careful steps to avoid it. Painting blue highlights on the model just seems like they were asking for trouble. Then again, for all I know maybe they did take it into account, knew how to compensate for it. But why not just paint it grey?
Anyways, back on topic.... I like the idea of it being the gap being a sort of miniature spacedock. One thing that the movies introduced that we never got to see in TOS due to budget and effect limitations were all the smaller ships: the workbees, the tugs, travel pods, warp sleds, etc. It makes sense that facilities are needed to maintain these vessels. Perhaps this area housed some of the TSFS/TVH style tugs we see around spacedock (which the only thing we may have seen towing was that Kirk & Crew's travelpod in TVH).
As far as the space originally being dedicated to Transwarp, in my personal continuity Transwarp was successful and became the "standard" warp in TNG -- explaining why all ships classes from Excelsior through the "D" have the "layered" nacelle style with the grey / blue glowing "with mint frosting" layer sandwiched between upper and lower housings. Which is just my opinion -- the Transwarp as a partial or complete failure are equally valid interpretations.
But if Excelsiors were the next generation of ships after Constitutions, I think it is safe to assume that many will be sent out on exploration / frontier peacekeeping missions, TOS style. So having robust resources would be important and be factored into the design.
It always struck me odd how in the movies, they depicted most of the lower hull being occupied by engineering and the shuttle bay. In TOS Engineering and Shuttle Bays were each confined to singular rooms (and yes, one can argue there were multiple engineering rooms reflecting the different configurations of the set, but we don't conclusively which ones or if any of them were in the secondary hull). I liked to imagine that the lower hull was filled with "science stuff" -- sensors, equipment, labs, etc. The revelation in TMP that such a large volume of that part of the ship was dedicated to the engines struck a dissonant chord for me. Any explanation that moves away from gargantuan drive system thingy, in favor of exploration specific purposes is more appealing to me. Star Trek, for me at least, was never about "breaking speed records" -- especially Warp Speed was basically as fast or as slow as the plot needed it to be from episode to episode. I want the ship filled with labratories, teams of scientists, botanists, astronomers, cartographers and the like analyzing stuff... WITH SCIENCE!! To me, the Excelsior was to (and by TUC did) herald a shift away from the Bennett/Meyer/Nimoy militaristic Starfleet back toward the peaceful scientific Starfleet of TOS. Design emphasizes this -- torpedo launchers are again recessed instead of sticking right out there on the refit-E. As much as I enjoyed the refit-E's aesthetic, that was something I had issue with.