"The Netherworld and Ghost Face are two different factions, though - I'm assuming the Crows are working for Ghost Face."

It does say that the Netherworld hired the Crow who blinded Zhao Yunlan, to specifically do that/to use any means necessary to open his Heavenly Eye. Which obviously doesn't mean that the Crow couldn't be working for both sides, and the other side just doesn't know about it.

"with potentially far-reaching consequences (see: timeline, and Kunlun not being blind!)"

Yikes, I didn't even think of this as one of the things that could unnerve Shen Wei about it, but of course it would!