While I don't do houses, I have been estimating for a little while. I think that with a little prep and a couple caveats, sq footage can be used for houses. First, fixtures other than can lights in kitchens, living rooms by others, second. incoming service conduit and conductors must be taken off. Third, must account for oddities, far side service, a well, and know whether electric or gas heat, instant water heater, etc.. So you can, say have a fixed price per ton for gas vs. electric heat. Per foot and amperage for an underground service. The number of rooms in the house is not going to change the cost to a significant enough amount that you can't just add a couple hundred dollars.
All that said, I would never square foot a commercial project, and I wouldn't even square foot a house until I had personally done a takeoff on a similar project.