There may need to be a little bit of manual intervention (to get the BA number out and the AA number into the booking) but once that's done benefits should be exactly the same as for a revenue booking that has the AA number in it.

Not sure if this shortcut would work (especially if the booking's already been made) but since Avios can be used to make a booking for any other passenger (unless you are a part of a household account - I'm assuming not), I should think that unchecking the box "account holder is travelling on the booking" and filling in your name, AAdvantage number, etc. would get around this.