How important is it that the building foundation be squared?

Not at all. you can fudge all the timber all the way to the roof to match the foundation other wise you would have a 4" overhang on one wall and a place to set your beer on the other. then cut back all drywall to fit the out of square rooms. if your flooring is hardwood or anything other than carpet you need to split the difference or lay it diagonally so you don't see it's so racked. then any furniture you put into the corners won't fit right or you could fire the contractor and get someone who can read a tape and check diagonals.