If you can get the seat for $650 plus some miles, I can't see why anyone would actually pay the normal 2.5k+ fare unless it is some corp contract. And then, why use/waste an SWU if its ranked the same as miles?

Along with some of the other things MSP posted about different upgrade instruments on the same PNR, it sounds like there was a lot wrong with the whole process and coding, and the redcoat just shoved it through at the end to get you on your way.