Almost all Deep Crypts I've encountered spawn half buried or just plain out in the open, see picture below

Minecraft 1.18.2
Forge 40.1.73
Structure Gel API 2.4.6
Dungeons Enhanced 3.2.1

you probably just got an unlucky seed
most of them I found generated buried

checking if they are exposed to air would require massive performance
I might find a easier way to reduce the exposed generation of dungeons in the future but for now we have to live with it