“Do you want any change?” is something I don’t hear a lot here, but it does happen occasionally.
It’s rude, but only because of this weird social construct in which we pretend that a tip is something we only give on special occasions to that unicorn server who satisfies all our dining needs in a way no one else ever can. The reality is, we’re probably leaving our change at least half the time, and many people don’t want their change back. On its face, his question is not unreasonable at all.
The other aspect of this is that he may never use this phrase, but you happened to get him in a thoughtless moment; I wouldn’t assume he says this to all customers. I remember when I was working in customer service; sometimes you’d catch yourself saying the weirdest, most out-of-character things, just because there are hundreds of thousands of transactions, and you’re going to say weird things sometimes.
Anyway, even if the guy was being rude, I’d shrug and move on. He’s already done his job at my table, and I’ve already decided on the tip before he even asks this question.