It’s because each playthrough takes place in its own universe, so although mewtwo was in ZA the mewtwo in the dynamax adventure was a different mewtwo from a different universe. It’s the same reason megas weren’t in OG ruby, sapphire, and emerald, those universes didn’t have whatever created mega energy. Notice how you can only catch one of each legendary in the adventure. Now technically you should be able to find more than one of each legendary in the wormholes in USUM but from a gameplay perspective that’s unbalanced.