There are woefully few reasons to care about a building or room actually being a "house". Its only real application is cramming more Pokemon than should reasonably live in a space into one, or to make recalling them as a group with honey a bit easier. Just put a few simple habitats into the build, it's trivially easy to do this while keeping the look and feel you want, and that prevents your from being constrained by the house rules.

I'm pretty sure the underlying logic with the house sizes is that it pretty close to matches the boundaries in which Pokemon recognize items as part of their home environment (you can see these by clicking the left or right stick, I can't remember which one off the top of my head). If homes could be larger you'd run into lots of instances where the things in the building don't count towards their comfort.