That would be more applicable to the last point that someone in the cabal is protecting him. It doesn't really speak to why the position exists in the first place.

If smoking man's goal was to protect Mulder, creating a department that directly puts Mulder in danger would be a bad way to go about it. There are dozens of other divisions in the FBI that would keep him busy and safe.

I think it was mentioned that the department existed so the government could say they were investigating stuff while sweeping it under the rug.

i thought the cigarette man was providing cigarettes to fuel the growth of the alien embryo inside scully

Use spoiler tags my boy. Most people who come through here will have seen it, but still.