When T'Pol resigned her commission with the Vulcan High Command, Enterprise was under the command of the United Earth Starfleet. I always assumed that at that point in history, entry into Starfleet was only open to people to citizens of United Earth and its various colonies. Unless T'Pol was to renounce her Vulcan citizenship and formerly enlist in Starfleet, she'd have to remain in a civilian advisory capacity, much like Phlox. She's part of the ship's command staff but outside the Starfleet chain of command.
^But the ship was still part of UE Starfleet in season 4, when T'Pol became a Starfleet commander. It was only in season 3 that she was a civilian, although in season 4 she wore the same outfits she'd worn in season 3 but with Starfleet insignias and rank pips attached.