Red Flags for DMs?

[Waker]

And why should the DM need to learn the rules of, say, incarnate or ToB in order to allow such a character? As a DM, I've allowed plenty of material blind, and it's worked out fine. I'm not the one running the character, the player is - it's the player who needs to understand the rules for their character.

The DM isn't strictly required to understand all the ins and out of a class. Some DMs may have issues of trust with players which is a separate issue. The player should understand the class they want to play, but it doesn't hurt having someone else know exactly how the rules for it work.
The greater concern I suppose would be in designing encounters for the party. If the DM can't accurately gauge the abilities of a class, they may end up placing the party in situations that are painfully easier to overcome or are inadequate to face.