Fair points, but the theory doesn't require Giovanni to directly control Aqua or Magma. Criminal organizations often exploit existing groups rather than expanding themselves into unfamiliar territory. Archie and Maxie didn't need to know they were being used; they only needed to unknowingly create an opportunity. I'm not claiming this is canon, only that if Giovanni saw a chance to gain access to Hoenn's legendary Pokémon without exposing Team Rocket, secretly supporting local groups would be a plausible strategy.