Separation physical and Disability physicals are two different programs used as two different tools for two different situations. A separation physical is kinda cover DoD ass later, so you can't claim disability later on them. Doing one shows that you were physically fit when separating from service. Kinda like wasn't broke when they left type deal. This is a program that only applies to member being discharged under normal conditions in full fit status. Members being discharged from duty under IDES program for reasons related to disability, do not fall under the SEPARATION HEALTH ASSESSMENT (SHA) PROGRAM publication DOD INSTRUCTION 6040.46 "The SHPE and SHA Program facilitate the transfer of care from the DoD to the VA and support the evaluation of disability claims. Service members suspected of having a medical condition that precludes continued military service will be referred to the Disability Evaluation System (DES), the Integrated DES (IDES) subject to the criteria described in DoDI 1332.18 (instruction quote: Disability examinations will (notice the "will", not recommended, not optional, but "will! as in the same as shall") serve as the separation physical if separation from military service occurs through the IDES.), or the equivalent USCG process. Service members not referred to these processes and otherwise qualifying for a SHPE are presumed to be fit for continued active duty, separation, or retirement". In this instruction, it even says the 180 to 90 day rule only applies to members not being discharged for disability. Doing a Separation physical after IDES and preparing to be discharged for disability can Screw you. Most doctors and military have no idea how the IDES program works and will make you do this physical and sign you off as you are fit, which while unlikely can undermine your disability ratings and be used against you in any dispute of benefits. So don't do it. Bring the instruction to your command/psd/admin/medical or whoever giving you crap (as most psd or admin will argue that you still got to do it cause they are just not familiar with the program and/or its policies) and the argument that doing this physical does not apply to you and can in the end effect your disability benefits, not to mention a huge wast of your time as you could be discharged sooner not having to wait for some appt.
Ref:
DoDM 1332.18-V2 IDES DoD Manual
DOD INSTRUCTION 6040.46
THE SEPARATION HISTORY AND PHYSICAL EXAMINATION (SHPE) FOR THE DOD SEPARATION HEALTH ASSESSMENT (SHA) PROGRAM