I think it has to be hand crafted with some mix of procedural generation. I worked on the Division Underground DLC, and the way we did it is we had artists create dozens of various room variations, describing how they could connect each other, then I wrote an algorithm to populate the map with these "dungeons" and their rooms in a semi-random order. In the end I think the map had about ~200 unique dungeons, but rooms could repeat between them, so you'd sometimes go "oh hang on I've seen this metro station before" but the entire dungeon would be different almost every time, unless you played hundreds of hours of it(the game kept track and wouldn't give you the same dungeon again until you played them all, iirc)