I personally believe Pikmin don't follow Hocotatians/Koppaites specifically because their space suits look kind of like a Pikmin. I think the Onion can kind of sense whether or not a being is hostile by default towards Pikmin or not, and depending on that allows them to command Pikmin.
Eh, mostly it's so cross-over fics/RPs can work, but still holds up if you believe the common theory back in the day that the Onion's are sentient.
I also believe Hocotatians and Koppaites are the normal size for beings in the Pikmin universe, and that PNF-404 (and by extension, humanity) are a land of giants. On top of the fact that there's two different species that are around the same hight, Olimar works for a space frieght company, and was heading to a vacation spot at the start of Pikmin 1. This implies there are even more beings out there that are around Olimar's size.
