One thing I can add here...if an AF pilot becomes medically disqualified and is not waived or otherwise placed back on flying status within a year, the USAF sends a letter to the FAA notifying the FAA that the pilot is medically disqualified. No specific information is given to the FAA, they just know about the disqualification. In the one case I know of, the pilot had an FAA certificate, not sure if notification happens in the absence of an FAA certificate, but I would guess it does.

If you have a disqualifying medical condition or history of one, don't fly as a civilian until you get it cleared up with the FAA. If you're not flying civilian, FAA isn't concerned about it.

Last point: in general, the USAF is more conservative in granting waivers than the FAA is in granting special issuances. If the AF is cool with what ails you, the FAA will probably be cool as well.