>>28493749They may have always existed as Pokemon, but that doesn't mean they always existed in the individual regions.
This is why they have Regional Pokedexs and National Pokedexs. Regional Pokedexs are the order that the Pokemon were discovered within that particular region, and the overall order for Pokemon Discovered is the National Dex.
So for instance, while Golurk may have been around for ancient times its only been recently discovered years after Gen 1, but for instance was discovered towards the end of the catalogging of Unova.
Types on the other hand are a different story. While Magnemite may be obviously Steel, they had no initial way to prove it, sure the type advantages and disadvantages, but that could have been assumed to been an electrical weakness for whatever reason. They didn't have any actual knowledge of what made a steel type a steel type, or dark or fairy, eventually Pokemon are reclassified when new information comes out. Think like the Wisdom Teeth, while they had a function in the past to grind up plant material, that is less of a think today, and so they have been reclassified to largely be useless, its sort of the reverse of that. We had no idea what they were for (whether they were steel or not), but eventually we learned they're used for grinding plants (they're part steel).
As for Megas we know where certain games take place and the game does say that there is an Alternate Hoenn. To the Dracos the meteor that inevitable contains Deoxy is dangerous and live threatening and they've harnessed technology faster, due to whatever reasoning, compared to the other timeline where it has taken them years. Could that meteor have destroyed things? Yes it is possible, it doesn't in the other timeline though, because we already see the meteor crash, it was part of a Gen 3 event if you recall.
I mean its not really all that convoluted, a lot can actually be explained within the Pokemon universe, barring stuff like Cubone and such.
