I'm not interested in addressing the Abramsverse ships, really, at all. I also don't need them for my purposes.
Since I seem to be the only one who IS, I'll add that to my "pet projects" queue.
From that analysis, however (inspired by King Daniel among others) I'm getting into the idea that there's no reason for the decks on starships to actually be continuous; and that a considerable bit of space may exist between them, which would actually explain the undercut for the saucer pretty nicely. That would mean some of the rooms/modules/compartments situated on those decks would have a bit of wiggle room for how they fit into the ship; a conference room might have a ten-foot ceiling while crew quarters are only eight, corridors are only seven, etc.
That might account for the lack of lineup between windows and deck spaces, especially if one assumes that some "plubming paths" built into the ship require parts of the deck to be raised or lowered to accommodate them.
The Excelsior model actually was scaled much larger than has been generally accepted, as I think I've proven. I'm following the logical conclusion of that to see what other classes scaled to match would be like.
I'm not sure that it matters, considering how rarely the other classes appear in the same frame with the Excelsior (and then only in DS9, which has widespread scaling issues of its own).
In this entire process, though, try to remember that length isn't nearly as important as volume. The JJ-prize, for example, is VOLUMETRICALLY about as large as an Ambassador class starship while even a 622 meter Excelsior would be about 2/3rds of that.