The rider stock OEM seat locks at the nose of the seat and rests on two frame posts just to the front of the rear fender - those three rest points prevent any down motion of the seat.  But there would be nothing to prevent the seat from moving upwards or sliding sideward if you remove the rear fender, or remove the rear bracket for the rider seat -- which would also probably allow the seat's nose lock to break off.  So yes there is a serious issue in removing the rear fender -- you would need to fasten the rider seat down (or install a springer seat) to prevent upward and sideward movement.