...In the TMP Enterprise, the rec deck is too tall to fit inside the rim of the saucer (due to that undercut thing on the miniature)
Not to mention the turbolift shafts where we see a lift coming down from the ceiling of a room that's on the topmost deck of the saucer rim!
Also, the aft compartment of the Delta Flyer from Voyager can't fit inside the ship, and there's no actual exit door on the exterior model.
Plus it has an escape pod somewhere, PLUS it has a 7-foot medical pod that retracts lengthwise
into the outer wall!