@gameragodzilla See the thing is though, you can do generation of plot important areas too, you just make the ROOM the encounter happens in the thing, and remember the rest. This is what most procgen games that have that do, Diablo for example since you're familiar with it, does this.
Hell they could have easily made it so that the FIRST time you go to the level, its full proc-gen except for the room Xing is in, and then it just remembers the level and repopulates it with enemies. This would be entirely doable in the engine I think since we see with the Free Roam mode after completion it saves them.
Part of the copy-paste feeling was having to fight girl-lass-whose-so-dynamic-I-forget-her-name-already's mutated body like three times too. The mechanics were the same every time basically.