I made this same point 1 year back and appreciate the OP creating the thread. I have given up with the hope that a flight with an A3 flight number and operated on A3 metal will credit to any *A FFP. I am amazed that each booking I have made initially shows an A3 flight number for the domestic segement yet each boarding pass ends up as an OA flight. While the segments/miles is a minor problem, *A baggage privileges (especially for HBO fares) can be a problem on a family vacation...especially when using the upgrade coupons on one segment (i.e. upgrading EU-ATH, economy domestic in Greece). Granted this gripe will lessen as PUT fares cannot be upgraded in the future, but it has been a problem in the past.
I look forward to Aegean bringing OA completely into the fold and eliminating the guessing game. I enjoy flying Aegean and will continue to fly them, but the advantage of using OA as suits them best has become an annoyance.