Littlefish - you should be OK. I booked a Gulf-US itinerary last month via AA.com. All BA operated but a mixture of AA and BA codes. I could book seats on the AA coded flights via MMB but not the BA ones.

I called BA and the agent couldn't work out why. She suggested I just check in online as early as possible. I politely insisted that advance seat selection was an advertised benefit of Gold and she was able to create a separate PNR for the BA coded flight and assigned me a seat on the upper deck. It involved a long-ish phone call, but worth it for the £1k+ saving over the same ticket on BA.com.