For what it's worth, my impression was that CX would let you do that once they've validated your itinerary. As you say, possibly will require manual ticketing - but perhaps the way to do it is to get a validated itinerary from the OW RTW tool and then ask them to change individual sectors once they've confirmed that the routing works. If you call the CX GCC's HK number, it is a cast of thousands and most don't even know what an RTW ticket is, so there will likely be a lot of HUACA'ing. Note that the Oneworld desk is based in HK and only works HK business hours (a non-point for those based in APAC, but for those in Europe / Americas, it means that any request raised through your local GCC and which requires Oneworld desk approval / pricing will have a lag).

The big sticking point for me was confirming validity of the routing (the agents are particularly oblivious to how second re-entry into continent of origin is permitted to operate, as is the OW RTW tool). Once CX's Oneworld desk finally confirmed that my routing was valid, the frontline agents were generally happy switching flights around different carriers etc provided the bones of the routing were unchanged. So I would hope for you that getting them to change to an AA metal flight to QF codeshare isn't problematic, subject to availability (and possibly more YQ/YR?).

Agreed! Sigh...