I've been tinkering around with the dungeons and stumbled upon a dungeon that overlapped with a stronghold.
I also found the enderportal in the dungeon. Except a lot of the portal frame pieces were missing probably because the dungeon spawn deleted some of them.

Could you maybe add some kind of "don't spawn within a certain radius of strongholds" feature or something? Cause I can imagine this becoming a problem in a survival game.