Wirelessly posted (BlackBerry: BlackBerry8530/5.0.0.1030 Profile/MIDP-2.1 Configuration/CLDC-1.1 VendorID/417)
"Spoke with EXP helpdesk and they said it's not possible to join revenue segments with award segments in the same ticket. If they are ticketed separately then the taxes are computed on origin/destination city pairs, and since you can't join revenue/award segments it wouldn't be possible to price it out as SFO-BLR and thus avoid the LHR origination/destination taxes -- or so they say at least."
Call AA back, and tell them to try harder. As long as AA can "see" the award flights on BA, AA should be able to put both bookings on a single "summary" of the bookings -- not a single PNR -- and not have to pay the APD to HMRC. But as noted above, nothing can be done about the fuel surcharges on BA metal, unless you can find a routing on some other partner carriers (like 9W, QR, or EY) that will require an additional connection somewhere.
Other FTers have reported not having to pay the APD when flying into London on a BA-issued award ticket, and then out of LHR on a connecting AA cash ticket from LHR to the U.S. If AA can do that, then they should certainly be able to accommodate you when both tickets (cash and award) are issued on AA stock.