I have what -should- be required to mutate Nitor Wart and bonemeal forcing mutations set to true, but I've stuffed six stacks of bonemeal onto the crosscrops so far with zero result.

Probably because it needs darkness, the plant will never sprout there when the conditions arent right.

how are we supposed to get it to mutate when the dark conditions make the orange tulip unhappy?

Mature the orange tulip in brightness, then when it is mature, make it dark, then it doesn't matter anymore for the tulip.