>>52431873in the final battle you can see the master ball from the time machine fall into the professor's hands and "catches the paradoxmon." it seems to me that it looks more like a magic 3d printer generating the pokemon.
and going all-in with the theory Master Balls are supposed to be incredibly rare, but the AI has a team of 6 mons all inside Master Balls. so unless the time machine is supplied with a bunch of master balls that go into the future and catch all the paradox pokemon, then the machine really is just hexagonmon's imagination 3d printer.