I was sort of playing with that concept myself at first, like, I made a shapeshifter, so, I wasn't sure if she should be allowed to have her shape shifting powers on top of two others... In the end, I decided to include the shapeshifting powers as one of her two powers, because even if it's a power that you get from your race, it is still considered a power. So, I would say that any powers within your race will be considered of your two powers... BUT... I am willing to allow characters to learn new powers as time goes on... But within reason. This just keeps the initial characters from being too over powered from the beginning. 

Keep up the good work peeps!