All your scenarios are correct and possible. I was told of the empty seats by the AA staff before our connecting flight. Not QF staff at check in or the lounge. So these seats weren’t any of the other reasons. QF agent specifically told me that the allocation for upgrades had been used.
In the same situation now as WP, I probably would have been upgraded just because they were empty. Not for plebs though.
this is getting OT and not to go on about this but..... I mean you've been given information some hours before the flight in question and from partner airline staff - I'm not entirely certain how helpful that is as much can change prior to departure.
As for what the agent told you (which I am assuming was at the gate?) did you actually know for sure those seats were still empty? For example, did you look at an EF seatmap? did you see them empty in flight? there may have been standby pax or anything.
I'm not doubting you or anything, it's just that so much can happen, specially in the last minutes before a flight as we all know and those seats could well have evaporated for various reasons.
or, it could just have been that sure, computer said no and again, if they were holding those seats for connections (very common ex-US) till the last minute then sure they wouldn't be offering upgrades in the hope those pax would show up.
I've been on many a flight - dom and international - actually sitting on board and watching the seat map change and fill - domestic it is usually deadheading crew, int it can be standbys, connections, late late upgrades, all kinds of things).
there can be many scenarios at play and competing priorities. As customers often we do not have the full picture (even with tools like EF) and may make conclusions based on information which may have been accurate at the time it was given, but may not reflect changes even minutes later.
imo