Each race starts with different technologies and abilities. However there are problems if you customize your starting race.

1) NONE of the races starts with 0 available ability points.

2) If you customize the abilities of you starting race, SOME but not all special abilities are lost.

3) Some of the racial abilities (e.g. Minimization, different logistics) cannot be duplicated in a custom race.

4) Some races start with certain technologies (e.g. Ion drive) without the needed prereq techs.

This makes some races superior as your starting race if you customize them.