The separate "bridge" and "attack center" facilities solve the most pressing of the TOS movie continuity problems. All that we have to wonder about now is cargo hold access: how did the whales get out, and how did the plexiglass get in?
We don't necessarily need a dorsal hole for the plexiglass: Sulu could have lowered the sheets to the ground, after which they were lifted into the ship through the same hole that let the whales out, and then lowered again into their slots. The cuts in ST4 allow for that. The cargo bay should just be two stories high, then, contrary to what those blueprints suggest.
But the ventral opening is problematic. Does the prominent belly dome split in half (like in the Defiant as seen in "The Sound of Her Voice")? Or is there a smaller hole just ahead of the belly dome, merely one bulkhead-to-bulkhead spacing long, through which the plexiglass sheets were jimmied in and the whales wriggled out of? It sort of makes sense to build a large "assault ramp" into the ship if it is already designed to bring warriors to surface battle as evidenced by the prominent wings and landing gear; it's not the existence of that ramp that is a bother, but its location...
Timo Saloniemi