Class creation question?

I am trying to figure out the game. I think that I have figured out up to Class creation. But the issue I am running into is for my base species I have the option of taking between three and seven traits, but then when I get to making my classes my level one troops can only have two traits. So if I took all seven that I could for my base species, then my level one troops who can only have two (and per the book "This includes class traits taken during the creation of Classes, from base classes, and after game rewards for future games." So do I have to drop one to five of them, and what does this do to there points? What is the point of making me take three if I can only have two on my level one troops?