The bottom of the flange should sit flat on the top of the finished floor and be anchored to it. This will put the top of the flange about 3/16 to 1/4" above the surface of the floor. If you can move it so it is 12" from the finished wall, then you will have more choices (and probably less cost) for a toilet. Make sure you account for the finished wall, and not just the studwall. My unprofessional opinion.