I've actually spent time thinking about that and the only thing I can come up with is that it's easier. Rather than having to do all this special stuff with payroll, just charge everyone according to one structure with all of its existing flaws. It makes it easy they to also add exceptions, such as making all combat-pay or hazard-pay tax free.
I would be inclined to agree with you if the tax code wasn't already a gigantic complicated mess. I don't think tossing in a few extra provisions would make it that much more complicated.