Besides, I don't think 'use doors to separate areas' is really that onerous of a restriction.
The point is that for a lot of forts it might not help at all, certainly none of the forts I make, which means you've added a lot of code for no good reason. This leads onto the point I think NW_Kohaku was getting at that your adding more ways players can try to optimise their fort rather than solving the problem. I don't think he wanted to stop players choosing to optimise, that after all is up to them, but just to avoid adding more code that only helps those that do and encourages you to.
Stairs would make more sense for my forts, probably, but doesn't sound like it would for NW's as he builds more vertical forts. Either way it doesn't sound like it's a general solution.
Of course I'm still not convinced path finding is the main cause of the frame rate loss, and if it is a single threaded A* search on such a small map should not be taking so long which implies it can be replaced without effecting too much.