[Theory] The Rodger Clifford Theory of Pokémon Mystery Dungeon Origin

Now, let me tell you something first: since Sword/Shield don't take place in Kanto, yet still lack a National Dex, there's only one way I can see Sword/Shield being in a timeline of any kind: the blast from the Ultimate Weapon split spacetime into not two, but three separate timelines. The third timeline starts with Detective Pikachu happening in parallel with Red, Blue, Yellow, Fire Red, Leaf Green, Let's Go Pikachu, and Let's Go Eevee. After Detective Pikachu, the timeline splits once more, with Sword/Shield happening if Tim Goodman wins in the final moments of the game, and Rodger Clifford is stopped. However, if Tim were to die in the fight, then Rodger Clifford, with vast resources and no one to stop him, would continue on to merge people with Pokémon on a global scale, causing the "Great Merge" and creating the "Merged Ones." A few people and Pokémon escape the Great Merge, and are known as the "Pure Ones." The people continue to run society with small adaptations, but then, an internal conflict ensues. Their Pokémon half is telling them that they can't go extinct, but their human half revolts at what obeying their Pokémon half would entail. The internal conflict gets worse and worse, and their Pokémon half is getting louder and louder. It drives them to the brink of insanity, and they give in only to not go completely insane. Their immense guilt is gone once the first eggs are laid, and when they hatch, the first descendants of the Merged Ones step into the world. Tales of life before the Great Merge are passed down through generation after generation, with society slowly morphing to accommodate Pokémon. Spacetime anomalies are forming everywhere. Eventually, a Whiscash founds the first town that is custom-tailored to Pokémon living humanoid lives: Pokémon Square. Hence the events of Pokémon Mystery Dungeon: Red/Blue Rescue Team begin.

Aetheral Meowstic presents the Rodger Clifford Theory of Pokémon Mystery Dungeon Origin.

It's a pretty good theory. Not sure what else to say. Figured you could at least use a LITTLE feedback :p
The only thing this doesn't answer is why the presence of these hybrid beings would be connected to the calamities, but even the games don't give a lot of details regarding that other than the odd story and pokémon being somehow certain of how to fix certain problems in the world. We don't know how many generations of pokémon it took for Pokémon Square to be founded either, so it's likely that it's not the first of such settlements--just the most well-known one in a large area.
This assumes that this universe is canonically connected to the main series, of course.