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I have to point out 2 possible corrections before proceeding, one of which already mentioned.
It's possible that the pixies of spirit were "created" (or better said divided) later on the creation of the multiverse, due to the mentions of them giving emotions, will and knowledge to humans, but humans were just like other mons before evolving into humans. Another hint to this is that it's said how they're born from the same egg, which still makes sense with the reconstruction of the Original One, but regarding the 3 dragons it's said very specifically how they "set apart" from the Original One. This reconstruction would also make sense with Dialga and Palkia being free in the past, and with the descriptions of Giratina being "banished", meaning that the 3 were only caged away when the pixies got created.
However it's also said how they bind time and space and in the story of the creation of the multiverse, which also says both matter and spirit 'make this world'. Thus still unlikely.
Little changes, but it's interesting because it'd mean that the pixies basically set humans apart from pokémon. It makes no sense that the pixies would be put out later on, but that means that tĥe mentions of their egg and of their life suddenly giving sentience to humans should be interpreted as a romanticization.
I'd say the timeline of the appearance of the pixies remains a mystery, although the first reconstruction stays the most likely.
