I think the AFI is ambiguous- especially given that what Ed stated is correct and is stated in several places in DoDI's. Here is what AFI 36-3212 says:
"1.4.4. Dual Action. Process as dual action, disability cases on members with an unfit finding
who are also pending administrative separation (including Second Lieutenants being processed for
"not qualified for promotion"), or who apply for nondisability retirement or discharge in lieu of
CM action according to AFIs 36-3203, Service Retirements, 36-3206, Administrative Discharge
Procedures, 36-3207, Separating Commissioned Officers, 36-3208, Administrative Separation of Airmen
or 36-3209, Separation Procedures for Air National Guard and Air Force Reserve Members. SAFPC
makes the final disposition. If SAFPC does not accept the retirement or discharge in lieu of CM
action, the CM will proceed. If the sentence does not result in punitive discharge, then the
disability case can be processed. NOTE: Administrative action continues in any disability case that results in a fit determination."
I doubt the outcome will change no matter how they process the finalization of your case. Likely, nothing that can be done until some final action takes place (if your disability separation is approved, you have the result you want...if they disapprove and process you for admin separation based on PT failures, then you will have to appeal to AFBCMR or in Federal Court). I would be shocked if your disability separation is not approved.