Problem with wall heights

I have recently learned of this limitation and, like the OP author, I find it frustrating.

But more than it being a frustration over the limitation itself (which can be circumvented by not building what you want, but what you can), I find myself frustrated by WHY the limitation is there to begin with. WHY is the game unable to distinguish between separate buildings, when it clearly can distinguish between rooms?

Is it because it considers the entirety of each floor of the lot as single rooms? I wish someone could explain to us the governing architecture and why it is so rigid!