OMG that's so funny about eyeshadow. "Shadow palettes"!
It's not due to different factories having different materials on hand. It's more like, in situations where Hasbro was like "Oh, this set isn't going to bring in as much profit as we want", they would use poly because it's cheaper in the literal "costs less money" sense.
That's why a lot of the ponies are discount chain ponies (lower price, not as much profit) or the "bonus pony" you would sometimes see in playsets.
I guess we should be happy they used nylon for most G3 ponies. I think it's going to be a disaster once G4s get a few decades out, the later years of those were definitely not made with nylon hair.