Residents are closely supervised by another physician. So it's not just paying for the resident, it's paying for the supervisor as well. And early on, the supervisor is going to be combing through the details of each patient to make sure mistakes aren't made.

That plus the throughput of residents is going to be much lower than a trained physician.

As such, Medicare pays a "training institution" premium for all billing. It's a small bomb (5%?) but pays for the resident.