So I load 500 on the GC, load 500 on GD and one is taxable and the other is not. Like I said, this makes no sense.
You're right (imo, anyway) that there is no difference between the two from a tax perspective. Both should really be taxed upon liquidation with the fees paid increasing basis and the reward dollars reducing basis (which the court basically says is the right approach).
However, the court decided to apply existing IRS policy to treat, where possible, the reward dollars as a rebate. That is only possible, said the court, when you are purchasing something tangible i.e. a physical gift card that has some other use/benefit to it. They declined to apply that policy to directly purchasing money orders. So despite the inconsistency, it's not a result of an inconsistent application of tax principles, rather due to an application of IRS policy.