Current flight doc here. I read the boards from time to time and enjoy it, so I figure that I should contribute and make myself useful!
Retirement or voluntary separation physicals are only required if the member has conditions for which he or she is seeking VA disability benefits (ie continued medical care, stipend, etc). All patient conditions which are specifically brought up by the patient will be discussed and examined. Specialty consultation may be required prior to separation. This physical and your medical record will be reviewed by the VA. The VA now does their own independent review and process. You should contact the VA rep in your med group to start this lengthy process immediately.
I see alot of pilots who are retiring in 6 months or so who come in with a laundry list of complaints which they have been stock piling. As a previous poster said, if conditions which are disqualifying for continued flying duties or retention (meaning MEB), you will be grounded and possibly boarded. This could hold up your separation, or your job in the reserves, civilian contractor flying DoD aircraft job, and so on so forth. If it is a legitimate concern, then by all means please discuss it with your physician. Just be aware of the above consequences.