That could be... themselves.

You're right. I vaguely remember a faux hijacking (or a real hijacking but not with the intent to do harm) wherein an unarmed man caused a flight diversion to seek asylum in Italy. He entered the cockpit while the door was open for service. I don't remember the details, but now I'm very curious if identification would have resulted in successful interdiction. It certainly would not have prevented 9/11 since those perps were known to both domestic and foreign intelligence. So what do we do?

To bring it back to the root question: how does REAL ID mitigate these threats?

Because it helps the TSA definitively identify whether someone is one of those people who are known threats. Prior to this standard, there were hundreds of different standards for IDs all with different levels of validation and there was no requirement for any cooperation in sharing information useful to validate them.