There is an actual explanation for the Phaaze-native Metroids: when the Pirates came there, led by Dark Samus, they brought some with them. This doesn't really explain the presence of multiple Metroid Prime corpses on Phaaze, that's a little element that's never quite sat right with me, but unless I've missed something major it's clear the Prime series isn't meant to be directly connected to the main plotline. It really is a side story in the end. I was a bit disappointed by this myself, but I believe that was the intent.
I haven't played Prime 3, so there may be very good reasons why this would be impossible. But if I were a Space Pirate and I encountered something awesome that I did not and could not control (like Dark Samus/Metroid Prime), I would immediately be thinking about what horrific experiments I could do to make one for myself. Maybe those corpses are the result of failed experiments to produce another Metroid Prime?
Of course, the second thing I'd do is create a detailed log of my experiments so that other