You are on the right track. Book the codeshare. I've never had an issue with an AA codeshare on QF.

By booking the AA codeshare as a first segment, you are making the OWE booking tool use AA to price the ticket versus QF. QF charges all sorts of nasty fuel surcharges and taxes that AA doesn't, hence the massive difference in price.

You can make changes through the awesome AA RTW desk. No issues there either. I've booked plenty of Circle Pacific's through them with no AA metal, only AA codeshares on QF/CX. They were happy to ticket.