So is the salient point coming out of this that booking a BA operated flight via aa.com no longer means you can choose your Upper Deck seat? (whereas fairly recently you could).
Heck of a showstopper for me if true. There are any number of itineraries I can't book on ba.com but used to be able via aa.com.
Looking at aa.com it does seem the BA flight number is no longer offered .... maybe that's the change? I used to take care to book the BA flight number.
Was OP dealing with the BAEC Silver or Gold lines?
Is the work around a price-match? Plan it on aa.com then phone up ba to book?