An update to this thread:
After flying the JFK-DCA-RDU flights, I emailed QFF asking for original routing credit for the originally booked JFK-ORD-RDU routing and got it.
On my later flight from RDU-ORD I had just reached WP the day before and was booked in coach. Looking at flightstats on the day, it showed several seats in F and A class. At check in I asked the lady about being put on the waiting list to upgrade into First and she put me on it. I was told to enquire at the gate before boarding (not at the A/C) and it was likely I would get it as there were still seats available. At the gate they called my name (same person who checked me in) and was presented with a new BP for First class.

It showed X booking class which I thought would not earn under QFF when flying AA:
Frequent Flyer - About the Program - Terms & Conditions
Looks like X is their code for AA EXP upgrades from Y to F on 2 class domestic flights:
Inventory Classes and Mileage Eligibility (AA) - FlyerGuide Wiki
I ended up getting credited for my original economy booking RDU-ORD (not the non-earning X class).
On a later BOS-LAX flight in Y, I asked again at check in but since F was full I didn't get upgraded.
However, once we were up in the air, the FA came up to me and greeted me, saying "You're an Executive platinum, we'd like to offer you a complimentary food item and coughtail". Of note is she didn't use the term "oneworld emerald" at all, instead "executive platinum". I didn't complain, so yes it looks like their system is not able to differentiate between AA and non-AA OWE members and groups them all as one... However at the A/C earlier when I enquired about F seating availability, the lady asked if I was using a "systemwide upgrade" and I mentioned something about Qantas OWE being able to upgrade into F. After making a lot of keystrokes she mentioned that there were several AA Gold/Plat/EXP on the list who were in front of me and it was unlikely for an upgrade...
So my guess is that on flights with low F loads, a non-AA OWE is likely to get an upgrade if there are few AA elites on the list.
What I'm not sure about is if an AA gold (OWR) has higher preference over a non-AA who has high oneworld status (eg QF SG/WP)?