Thanks Calchas for the very informative response. Perhaps an edited version of your response could be considered for the wiki for easier future access.

I have been doing some more research. I include below some findings that might help future readers.

Not all AA codeshare flights listed on the AA PDF Timetable show up on ITA/EF, including some of those not requiring specific connections. And I am not quite sure why. But from the ones that do show up on ITA:

AA codeshares on QR do charge the same YQ surcharges as QR metal. So in this case, AA seems to be passing on the exact same YQ surcharge as the operating carrier.

CX codeshares on QR charge a lower YQ surcharge from QR metal. CX seems to be charging their own (lower) YQ surcharges rather than those of the operating carrier.

Have not checked other OW partners, but will do soon and will report any findings worth posting.