Hmm... actually the contour of the separation plane in that sketch does seem to clash with the shuttlebay proportions shown in the MSD cutaway. But of course it's just a concept sketch, not actually binding. If the "steps" pattern on the top of the lower portion were shaped differently, dropping off faster from back to front, it could correspond to the shuttlebay underside seen in the MSD.
And as I said above, I don't assume the MSD cutaways themselves are absolute gospel, since they're just set decorations meant to convey a visual impression. If anyone ever wrote a good script that required making assumptions about a ship that contradicted the MSD, no sane producer would ever say "Sorry, we have to scuttle that story because it contradicts a few barely visible lines drawn on a piece of set decoration."
Heck, if the TMP Enterprise can have a rec deck that can't fit inside the saucer and an engineering corridor that extends farther forward than the front of the hull, and if a TOS shuttlecraft can be bigger on the inside than the outside, we pretty much have to accept that the proportions of fictional starships are intrinsically ambiguous things.