Thanks for the tips here. My experience with an AA ticket, 2 AY operated flights, one AY flight number and one AA flight number:
- Used AA booking ref to find the AY booking ref on aa.com
- Entered AY booking ref on finnair.com to add BAEC number to open up free seat selection.
- Used AY booking ref on rj.com to select seats for AY flight number, AA flight number did not work
- Used AY booking ref on royalairmaroc.com to select seats for AA flight number which worked fine.
I think the RJ trouble may have been because the AA flight number said the aircraft was A350, but seat map is A330.