I bet this is one more of those stories for which we're missing most facts. I have plenty of musician friends. The way they travel would totally fit the OP's description.
Guess what... they pay for an extra seat for their instrument. And they're as entitled to their carry-ons as you and I. And nope, instruments don't earn miles.
Of course, I could be wrong about what the OP has witnessed. But "E+ and even 2 FC bins are stuffed before anybody else is on" -- no way I buy this.