I think his question is, if he doesn't apply his Aegean FF# to the flight (where he would have status), instead applying his UA/CO FF# (where he does NOT have status), he would not receive the *A Silver benefits, right?
I think his assumption is correct here, because without using his Aegean FF#, the airline has no idea what his status is in that specific program, since having status in one *A program doesn't automatically transfer over to all your other separate *A programs you may have signed up for.