Well, the point of Flying Spaghetti Monster was getting baseless religious dogma out of schools by offering up an extreme/absurd example of what allowing Intelligent Design into any kind of official procedure was implying. FSM seems like it should only be pulled out when pointing out that the special considerations made for religion are absurd.
Getting it recognized as an actual religion means that you've just made an actual religion that no one believes in, -at best-. At worst, you're implying that no religion has the right to be recognized because it's absurd. (Although, I suppose some people may agree with that last statement, it seems a bit extreme to me.)