In my limited experience, AA RTW desk will be completely fine with assigning AA flight numbers but only if the other airline allows it. I don't know the logic behind what works and what doesn't, but AA has said that travel agents can book AA codeshares when AA themselves cannot. They also said that they can get the AA codeshare on routes that "touch" the US.. but everything else -- YMMV. Never hurts to ask if having the AA flt number is important (which it is, for AY earners).