Flying PE will likely give you more SC over flying Y on the QR flights, VA coded or not. Though going to Europe I think you no longer have the option of a SQ flight on VA codeshare.Any considerations re status credits
You can redeem KrisFlyer points to upgrade a SQ flight if ticketed directly with SQ. Similar offer is possible with QR using Avios/Cash if booked directly with QR. It's unclear if the same option would be offered to VA flight operated by QR.opportunities to upgrade (points or pay)
TBH premium economy will be much more comfortable than econcomy for a trip like this so I wouldn't even consider QR economy if SQ PE is an option. Also I suspect you can probably get a flat bed business for not much more than SQ premium economy if you take a slight detour and use non-premium Asian (Vietnam,India,China) carriers which often advertises cheap connecting fares to Europe from Australia. I'd pick a flat bed business over economy/premum economy of a more premium carrier any time.
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