>>46334886cubones happen when a kangaskhan dies or they just get born from other cubones/marowak
mimikyu are just all very jealous and since pikachu is the most popular pokémon, they all dress like it
porygon is digital so multiple can exist. porygon z is just an updated and then corrupted version of it
banette (like cubone) started as a possessed doll but new banettes can be bred
the weather trio are just very powerful and rare pokémon but multiple can exist
I don't think multiple Zygarde exist, its just that canonically the cells hang around all around the world and each game is its own universe, so there is just one per universe
Spiritomb are just different trapped ghosts.
Elgyem are aliens
Type-Null, castform, claydol, genesect and magearna are artificial.
Reshiram, Zekrom and Kyurem are products of a dragon, of which multiple could exist. if not, same thing as zygarde, there is one per universe but you could have two through trading because each game is its own universe
other legendaries, like Xerneas, Yveltal or the Sinnoh legendaries have the same thing going on.
There are multiple Mewtwos since, again, artifical.
Electrode/Voltorb started of as alive pokéballs and through breeding they are available in the wild
The rules are basically either a legendary is just a rare and powerful pokemon or they spawned through a specific event (like cubone or banette) but those then bred and made more