There are labs done with flight physicals that aren’t done with a DODMERB exam.
For example, for flight physicals, they will see if you have anemia by checking your hemoglobin and hematocrit levels. Your urine will be checked for blood, protein, and glucose. Your blood sugar will be checked too.
An EKG will be done on a flight physical which can be another source for a DQ.
Finally, your eye exam will include a cycloplegic refraction which is not done on a DODMERB exam (only a manifest refraction is done). Eye drops will be used to paralyze your eye muscles so you cannot accommodate. This basically means you won’t be able to change the focusing powers of your eyes to help you see the eye chart better. A cycloplegic refraction gives a more a true picture of your eyes’ refractive error which can lead to more DQs for flight duty.
There are a bunch of other ones but the above are the primary examples.
But to clarify, what I’m saying above is a description of what’s done during the flight physical done at the academies during the 3rd or 4th year. I’m just pointing out some of the differences between a physical done specifically for flight duty and that done for DODMERB. The purpose of the DODMERB exam isn’t to qualify or disqualify for flight duty, so there’s an inherent difference there.
As an aside, one of the things they do on the DODMERB exam that isn’t related to academy qualification but it is for pilot qualification is the anthropometrics. It’s when the DODMERB doc (or nurse) will measure your sitting height (a dedicated flight physical will also measure leg length and arm span).