Yes, it's hard not to notice how the elevator and the maintenance passage seem to be some ten times farther apart on Engineering than they are on Med/Sci. Though, I think that this kind of inconsistency is still, if barely, passable (and probably stems from the fact that the various decks were designed by different people from LGS/Irrational). You could even attempt to justify this by implying the presence of an unshown horizontal passage between the endpoints of the maintenance access, even if this would come across as a bit (literally) "stretched"... compared to this, not seeing the upper side of the VB and the Rickenbacker from the VB bridge is in my guess a more blatant inconsistency, even if it doesn't jump at you immediately.
I also noticed how the the labels "port" and "starboard" (essentially meaning "left side" and "right side", respectively) are reversed on the Engineering Deck map showing the coolant/engine section. Assuming they were correct, it would follow that the engine core and nacelles are at the front of the ship, which makes very little to no sense at all (for instance, the "front" view of the ships' bridges would turn out to actually be facing the rear).
Now one could start a debate on what the protocol droids were on saying that "this place is a terrible mess"...
Well, when you think about it, the flaws between the designs and the actual product may simply be blueprints or beta stages left by LG/Irrational to hint that the Von Braun perhaps went through a test run under a different name with a different UNN vessel to test a different set-up. That could explain why the Von Braun wasn't very complete when it set off on its maidan voyage as a number of changes had been made to refit it for the final model. (If you remember in the beginning cutscene, the map layout of one of the decks was dramatically different from any layout that we seen in any deck during the game, supporting the idea that it was refitted for something compact probably).
Also, if you've played Dead Space, the horizontal/vertical elevator actually does make sense. Think about it for a bit; the decks are all probably organized in a way to be compact and leave no oddly empty spaces (the layouts of each deck are pretty different from one another and so, simply layering each deck on top of one another would create a very odd-looking hull and leave quite a bit of empty space).
That's my theory so far.