The people upstairs who review TO's, and scoring plays should also be looking for clearly blown calls. The play is already stopped for the penalty so it wouldn't take much time. Of course this should only be on flags thrown, as that is an official interference into the game rather than looking for penalties that should have been called but were not.
Either that or like you said above make these penalties challengable under the same challenge limits.
Edit: On another note, if these are all "legitimate" flags and the officials are just calling them more (noticeable uptick in flags thrown), then maybe the rules need to be changed. If football was more enjoyable with less flags, and players presumably getting away with fouls 5 years ago that they aren't now, then either change the rules or tell the officials to lighten up. Just my 2 cents, flag football is no fun.