>Similarly, something could be concealed by magic, which dwarves aren't good with.

Dwarves would detect a door by more than just where the door is. They assess a room and are able to tell by the design if there should be a door in a place.

>It's possible we could mark doors with some sort of dwarf-detectable flag, or hope that area writers remembered to assign a correct material to their door, and have it only work on doors made of stone.

Being made of stone isn't too important in my mind. It has more to do with dwarven affinity for architecture as opposed to an affinity for earth/stone. I can't see any harm in making this more open-ended, allowing them to see everything except specially marked doors.