Loss of racial traits

Go ahead and hit clear to get to your race defaults. I like using the thalan empire to see the effect.
You get 40+ loyalty by default if you click on "abilties" you have two unspent points. If you put 1 of those points into Loyalty-"mostly faithful," instead of you total loyalty becoming 50% it changes to 10%. And that is what you start the game as.

So the prob is, this stop people from spending ponts in loyalty with the thalan and yor collective etc. If you spend you points elsewhere you can keep the +40 or +100 loyalty bonus but if you try to bump 40 to 50 you really lose 40 instead of gaining 10.

It is the same for all other stats that don't start with some boxes checked in your abilties screen. Most noticable with Torian morale that is how I confirmed it was cosmestic. If you hit clear torian's have +25 morale. If you spend your extra points to try to bump it you lose the advantage of the natural +25. So if I spend 1 point for +10 instead of 35% you end up with 10%. But if I send that point somewhere else you will get the +25% plus whereever you spend that point.