He could be a general Republic protocol droid used by the Feds.

I did suggest in my earlier post that one of the Feds is obsessed with the Queen living long enough to sign the treaty and Threepio is programmed for a secret mission to protect her (reversing the role Artoo had in ANH).

He could even have a homing device placed inside him which is how Maul manages to track them.

He could even have his coverings removed to try and track the device down (giving another reason for See Throughpio).

So he could find himself indirectly trying to influence events to that goal.

When the treaty no longer becomes an issue his other mission which is never countermanded becomes so embedded that he becomes a valuable asset.

He could remind the Queen about potential of the Gungans so the scenes in their underwater city become redundant or it could be replaced with a different kind of city which the Federation could destroy.