I don't think the Nopon means anything, just like Chocobos and Moogles being in more than one Final Fantasy doesn't mean anything. The Nopon will probably just become Monolithsoft's mascot character.
Zanza
They, by proxy, would not exist before the events of Xenoblade. Sure, they may be Monolithsofts' mascot - but they've only appeared in one game, where their origin was made explicitly clear.