Just to close the loop on this for anyone who encounters the same issue in the future – even though the answer is still not 100% clear.

I ticketed the new flight after the back office fare calculation and was charged the lower 75pp number (157.5k for 2pax + infant), however the avois charge on my ticket e-ticket receipt is 200,550 (which is a completely new number…).

There was also no tax difference calculated even though I’m think there should have been maybe a £15 refund.

So, assuming there is no Avios adjustment at a later date, it seems that even with a stopover the online QR based pricing is the correct value.