Presumably AY receive an amount of money from QR for transporting you, so it's not impossible they could base a calculation on that. But as you say, the discrepancies have predated AY's change to being spend based.

The variations sound a bit random so no wonder you are confused. The calculation must be based on something though.

Have you tried dropping a line to the AY loyalty scheme to just ask in general how they award codeshares now they are spend based? It might get nowhere but you never know...