The first DONE3 I got was with the old version of the tool and when QF did ticketing for JL.
QF Japan had problems charging my card due to a per day card limit I didn't know about. They saw that the billing address was in Australia and had QF Sydney contact me.
Once I worked out what the problem was and lined everything up with the bank, I contacted QF Japan via QF Sydney and it all went through - still at the Japan price and charged to the card in JPY.
The country of origin vs country of sale rule existed at the time, and QF still charged the JP price knowing full well that I was in Australia at the time (though I ended up paying more due to currency fluctuations and the delay in getting it all worked out).