Mostly it's ignorance. They see one category that is mostly filled with G4s, they know their pony doesn't look like that, so they stick it the "non-G4" category.
Honestly, we are very lucky to have separate categories under MLP at all. Transformers used to have several categories but then eBay mashed them all together. In fact, it's not only just for Transformers anymore, now it's "Transformers and Robots". I pray that eBay never notices that MLP still has two separate categories.