Or it could be that, while every other planet maintains some form of independence, Earth is actually wholly UFP territory, and thus the UFP prez is directly in charge of Earth!
Not only is that not true, it would be inconceivable. It would mean that Earth citizens had no rights and no representation.
Just ask anyone living in Washington, DC why that would be a problem.
As for the eps in question: There were supposed to be scenes where Jaresh-Inyo "federalizes" United Earth personnel but it got cut for time.