for example: the 'official' tag for a pairing would be Fox Mulder/Dana Scully. a writer might tag her fic as Dana Scully/Fox Mulder and a reader might search for Mulder/Scully. but they're all the same thing. (or they will be, if they haven't been syned yet - i don't wrangle XF.)

Yeah, but a reader might (for example) want to find fics that are Mulder/Skinner and not Skinner/Mulder. As I understand it, AO3 currently wrangles them as the same pairing, which is a classification that might not work for everyone.

I will indeed send my suggestion to support!