After the events of 3 and 4, I'm looking back and realizing that we REALLY jumped to conclusions on Gaster being the one making the schizo bosses and leaving Shadow Crystals.

Like, from everything we've seen of him in actual canon, that really doesn't seem to be his deal at all. It's far too hands on for a guy that seems to be unable to maintain a solid form in the world.
It makes way more sense now to consider it being the Knight's doing, just like all the other shenanigans in the Dark Worlds. The Knight seems to HAVE to follow the prophecy, so the Shadow Crystal stuff could be it's own ulterior motive, a challenge to try and get us to rise beyond the story by getting these dangerous super bosses for us to fight. It even gets us the Shadow Mantle so we can get a good fight against it directly and nab one from it in the clash.