An additional datapoint on this. I made an award booking in BA business class USA to UK, using miles from JAL Mileage Bank so the booking record held my JL frequent flyer number. I was unable to change that at any of the usual online sites so I telephoned BA and asked them to add my AAdvantage number... platinum so OW Sapphire.

Now when I go to ba.com it still shows my JL FF number, but now says I can make a seat selection free of charge. However when I try and select seats it would bounce back out with an error... I could see the seat map, I could try and select a seat, but it failed to confirm.

So I telephoned BA and had them assign seats for me. That worked, the agent could see that I was OW Sapphire and so eligible for free seat assignment. However he could not (or would not) assign me seats on the upper deck of the 747. So while both ba.com and expertflyer showed open seats on upper deck, agent claimed none available, or that they were reserved for airport assignment.

DAK