I expect Qantas' implementation of SC earn for Points Club isn't smart enough to differentiate between the two - but I hope
@_flyer posts back with the outcome.
When an upgrade is requested, a SK FQUR element appears in the PNR. This SK FQUR element holds the FF number of the sponsoring member.
You can tell whether your PNR contains a SK FQUR element by looking on QF MMB. QF MMB will say "Upgrade Status: Requested" in the flight info section. The lack of presence of this "Upgrade Status: Requested" means there's no SK FQUR element and therefore no upgrade requested.
When an upgrade is processed, a SK FQUG element appears in the PNR and the SK FQUR is removed. This SK FQUG element holds an upgrade certificate number. The presence of this SK FQUG is what tells the system that you upgraded with points and it tells the system to check the upgrade certificate which tells the system what your original class was eg. O, Q, N etc.
On a classic award, there is no SK FQUG element. Therefore by default, the system assumes X/U/P/Z classes are classic awards. The presence of the SK FQUG element is what tells the system to stop and re-think.
This SK FQUG is used for both commercial fares upgraded with points and classic awards upgraded with points (eg. where you book a U class award and put in a request to upgrade to F).
Therefore I would expect a correctly processed commercial fare upgraded with points for a points club member, to credit according to their original class whatever that may be.
You can tell whether your PNR contains a SK FQUG element by looking on QF MMB. QF MMB will say "Upgrade Status: Confirmed" in the flight info section. The lack of presence of this "Upgrade Status: Confirmed" means there's no SK FQUG element.
A real world scenario where this is important is when you have a flight that you've upgraded with points and that flight gets cancelled. If the system auto rebooks you, then the SK FQUG element gets moved accordingly. However, if you get manually rebooked to another flight (eg. if you didn't like what the system rebooked you to), then the SK FQUG element does not get copied across.
This results in the flight info section no longer showing "Upgrade Status: Confirmed". The outcome of this is the flight you upgraded with points, then credits as a classic award. For non points club members, it'd credit as zero. For points club members it'd credit accordingly at the prevailing rate eg. 18 for a SYD-MEL. That then obviously requires contacting the FF service centre to fix.