The "Man Trap" reference especially would seem to make the "levels are parts of an Engineering maze" interpretation vastly preferable. If it's anything like the STXI facility beyond those neat and tidy control rooms, then a "level" is probably very different from a "deck", and in practice represents an odd "fraction of deck".
The one canon view into the TOS engineering spaces, the Drexler diagram from a parallel universe, indeed suggests loss of deck structure coherence when one moves down to the Engineering Hull. It's probably restored in the after parts of that hull, though, making it particularly valid to label one of the decks "Hangar Deck" specifically: little else but the hangar is to be found on that deck, if the corresponding forward hull spaces are but a jumble of catwalks.
The one thing we probably don't need to bother with is attempting to keep curved corridors away from the secondary hull when assigning identities to named and numbered decks. We have to accept that the sets "lie" to some degree in any case, as the ship just plain cannot have circular corridors of the exact same curvature or radius; sometimes the set has to be interpreted as having shallower curves than it actually does, sometimes sharper ones. The Engineering Hull might feature lots of "shallow S" corridors snaking past bulky pieces of machinery, say.
Shallow curving might also be necessary in the problematic hull support pylon: a straight corridor running down the middle would divide the space into uselessly small halves, but a corridor curving along one side would leave maximally useful rooms on the other. Not that too many decks in the neck would have corridors - but Deck 12 just might.