So the only way to get this is to level without ever doing the MSQs on one class then switch to another class and do the MSQs on that so you get the bonus?

Who would do that? Why would they make you not get the bonus on the one and only time a character would do the MSQs, the first time through?

Once you have done them on a character they are gone, so sub classes get nothing, seems like a way to just not give the bonus to me.

Or does it affect other characters that you start as alts? If that's the case it about as useless as the other method.