The unfair advantage argument definitely holds water, mouse and keyboard can be like a sports car racing against a bicycle. But if someone had the budget to tackle this issue through software, it would be Microsoft. So I’m inclined to agree that it’s mostly just MS squeezing money out of third party manufacturers.
If they’d care only about the “unfair”, they’d put a fair, almost free, price on the official license that covers the cost of testing or whatever. Truth presumably here is also a bit more complicated, maybe third party controllers could be easier to hack resulting in an ineffective licensing system, idk. But yeah smells like money for Microsoft and a loss for consumers.