I just made a Lost Cities + BOP world a few days ago and so far I'm liking the post-apocalyptic world gen and feel. The problem comes when one tries to find AS shrines to get going on this mod. BOP makes it hard enough to find extreme hills and deserts ordinarily. Lost Cities seems to do the rest of the job and when those biomes do show up, coat them in city with no prayer of leaving behind an AS temple. I've flown around the OW for a few hours in creative and have yet to find a shrine. Is there a way to make Lost Cities not stomp on AS shrines?

No I'm afraid not. I have no control over spawning of AS shrines and also no way to detect that they have spawned. I can think of no way to solve this except reducing the rarity of cities so that there is more normal landscape for the shrines to spawn in