Why not? People aren't stupid, and I expect most people realize that some businesses aren't meant for YC for one reason or another. Trying to obscure that fact doesn't make YC better, or more appealing. I'd actually say that covering that material would make YC more appealing, because it would hammer home the point that the YC people are on-the-level, straight-shooters who don't try to distort the truth to favor themselves. Who wouldn't rather do business with somebody like that? It's basically about trust.
You could almost make a comparison by analogy the old saw about how "the best way to get customers to use your product is to make it easy for them to leave your product".
So the YC course would talk to people about advantages of not going into YC? Hm.