For what it's worth, I think you might be forgetting one crucial part of the equation: history. Most buildings in the world today, and most buildings that have ever been created, were not designed. People build what they need, when they need it; it was only the rich and powerful who tended to add embellishment and design to their structures. Thus, a simple rectangular house - possibly only one room - is not only a plausible design for a building, I'd wager it's also the most common historically.

The key factor, though, is that the rectangle might be extended at some point, based on needs and circumstances: a new baby in the family? Add an extra room. A new tenant who makes pots? A kiln/workshop might appear. Through processes like these buildings can evolve over time. It is relatively rare that a structure will be demolished when use changes, as it is so much cheaper to keep what is already there. The interesting thing about this process is that the building form does follow function, but the function changes, and so the building becomes less and less coherent.

So my advice to you: design your buildings so they look undesigned.

Another piece of advice (for all mapmakers): what looks boring on a sheet of paper (a rectangle, a grid) would not necessarily be so in reality. The addition of doors and windows, brickwork, furniture etc would obscure the simplicity of layout, as well as making the place look 'lived in'. That, I think, is why isometric drawings/maps are so popular here on CG.