Wirelessly posted (BlackBerry8530/5.0.0.601 Profile/MIDP-2.1 Configuration/CLDC-1.1 VendorID/417)
"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"
If we're talking about benefits like free checked baggage or (for Gold) free lounge access, the Aegean Miles + Bonus membership card, showing Star Silver or Star Gold status, will rectify the partner carrier's ignorance.