I am guessing here, but if the floor is concrete that means the carpet is glued down and is difficult to remove cleanly. The bolts/nails to afix the studs must be "fired" into the concrete with a special nail gun (yes, it is fired into the floor). I would expect that it would be much less time consuming to go over the carpet. Later, the carpet can be cut away from the wall. This is much easier for the contractor and less expensive in the long run and I really don't believe there is a problem doing it this way. I would call my local village office and get another opinion just to make you feel confident in your decision. Good luck!