Haviing all BA flight numbers and buying a 125 coded ticket results in slightly more Avios but for Premium classes F and J the tier points will be the same.
However I am finding that for F itineraries, AA is more often than not considerably cheaper than BA even if the exact same flights are chosen. I think this is because under the JBA for transatlantic traffic AA has access to all the BA transatlantic flight seats and vice versatility. However, for domestic US flights AA has more availability and can offer fare basis which BA cannot. This can result in a very significant fare difference - I have seen differences of over £2000 between identical itineraries. Not surprisingly, I have booked the AA one.