Hoenn and Sinnoh used to be part of the same landmass. Because Regigigas wanted to seal itself, most likely yet again from a struggle between humans and pokémon, it separated Hoenn from it as far as it could long ago, leaving the Regis and their people far from it in the sea. This civilization was back from the Stone, Ice, and Bronze eras, hence the Regis were made to commemorate the times they lived with Regigigas.
This accidentally caused Groudon (who slept in Hoenn's landmass) to invade Kyogre's territory, thus making it a matter of time they started their apocalyptic battle a second time. (Of which there were three: One far before humans in the early stages of Earth that reshaped the world, which Rayquaza stopped late or built a better atmosphere after; this one, which threatened to reshape the world again but was stopped by Rayquaza this time around after plenty of damage was done and is the one humans saw; and the contemporary one in the events of Emerald)
Likewise, that long ago Groudon lived in a time and location Heatran were common. The Heatran in Sinnoh is/are what remains of Groudon's home. Heatran is a pokémon from back when Earth was mostly magma.
Lati@s rarely separate and venture into known and populated places, preffering to be secretive among other of their kind. This means the ones you find are involved in something for this unusual behavior, with one of them looking for the other (preassumbly meaning they are acquaintances of some kind), while the other having gone on their own accord for something (which will never be known because GF cut their story out). In RSE, the one roaming Hoenn is actually looking for the one that has a Soul Dew in a relatively nearby island. In HGSS, the one with the Soul Dew has come looking for the one that is roaming, which has come looking for something else.
Jirachi's true self is actually only the eye. Back in RSE, it was open, signifying it was awake (for it's thousand-long sleep). In all subsequent games, it is closed because it's sleeping. The rest is a minor fraction of Jirachi's consciousness to keep it capable of action while its true self and mind sleeps.