Most don't put magnifying optics on a flat-top but use something like an EOTech red dot sight. Or if they do put magnifying optics they mount it high, on the handle or above the height of the fixed sights. The front and rears don't interfere as much then. Better yet, and what I have, is a DPMS front gas block with a picatinny rail on the top, on which you then mount either flip up front sights or at least removable ones. Then they are out of the EOTech's (or whatever red dot sight you like) sight picture without trading off scope height. You can use flip ups as a back up to a scope if reliability is important.
Fret not though, a conversion kit from pic to weaver rails may provide the needed height boost to ensure the fixed sights are sufficiently out of the way of the scope center. You lose a little as the further you get away from the barrel with the scope, the faster the accuracy (not grouping accuracy, but accuracy of the scope) drops off as you move away from the yardage you zero'd the scope at.