Some of the ten major races actually have left over points that can be used to further improve the race. You can remove also some of the bonuses, to gain back points to use. To the limit, you will end up with 10 points to use for all major races once you remove the selectable bonuses.
You will notice that for most of the major races (this includes the 'custom race' slot), they are also spotting bonuses that aren't selectable or deselectable.
Firstly, all of them have logistics bonuses between 5% to 8% and some like the Yor Collective and the Thalan Empire have Miniaturization bonuses as well. These abilities are neither selectable nor removable.
Secondly, most of the races will be showing some inherent bonuses at values that cannot be normally selected. Take the Thalan Empire , you will find that they have a Loyalty bonus of +40 even though such an option is not selectable (you can normally take only +10,+15 or +20) or the Drath Legion who have a Military production bonus +25 when the normal selectable bonuses are +10,+20,+30 and +50.
Same goes for other races, like the Terran Alliance, Drengin Empire,Altarian Republic etc. , all of which have their own inherent bonus in different areas. The only exceptions are the Arcean Empire and the Iconian Refuge who only have logistics bonuses and nothing else.
This inherent bonus will disappear though if you try to select a bonus in that category. For example, if you play the Drath Legion , they have among other special bonuses a inherent Military production bonus of +25.
However once you pick any bonus at all for a Military production bonus (whether more or less than 25) , the +25 bonus disappears (the other inherent bonuses are not affected) and you are charged normally for the bonus you selected. Obviously it makes no sense to pick any bonus less than 25 since you are just hurting yourself. And for most part it is inefficient to select a higher bonus, because you lose any benefit from the inherent bonus since there is no discount and you are charged normally for that higher bonus.
Comment: I do believe the above has been changed for (at least) the Gold Edition of the game, inherent bonuses and racial bonuses now stack, instead of being eliminated.
In both cases, you get 10 points to use plus the logistics bonus.
Besides alignment (some hardcoded hostilities?) and slightly different starting techs (both of which you can't change), whatever you customise for one, you can do so for the other.
Also for most part, the Drengin Empire who also have a logistics bonus of 7% and a further more an inherent Morale bonus of +25 will be superior compared to the above mentioned races for customization (again excluding slight differences in starting tech).
Whatever setup you create for them, you can always do better playing the Drengin.
Similarly, the Yor Collective look better compared to the Iconian Refuge and the Arcean Empire for customization because they have a higher inherent logistics bonus of 8% as well as inherent bonuses of +25 miniaturization and +100 loyalty.
Comment by p22, on Iconian Refuge
Iconians start with class 14 planet, so there are reasons to choose them, if you want strong homeworld. Also their starting techs are pretty good.