I've carried mtn bikes in the back many times but I've always folded down the seats and put down a towel over the bracing due to the sharp edges.
My bikes are freeride and downhill types, with long travel forks, wide bars and wide tires. I've never tried to do it with any of the wheels mounted on the bike. Since they come off easily why fight and struggle to get the bike in with them on, and risk scratching the car up?
Recently I got a class 1 hitch installed and now I carry my bikes on the back.