I think a case could be made that upgrade fees are not ticket purchases. On United, for example, they have a whole raft of "Options" that you can add to your existing reservation after the ticket is purchased, from "Premiere Access" for check-in lines, "Award Accelerator" for extra miles, and "Premiere Seating" aka upgrades. In terms of how they are presented and managed, there is no difference between these, other than the price tag.
I think based on the langauge above, they could exercise the "reserve the right to determine which purchases qualify" which gives them lattitude to do pretty much anything.
I WOULD agree that an instant buy-up offered while buying the ticket would be a tougher sell.