Well, the idea is allowing the designer to ask those questions and give the system enough flexibility to let him/her build the required character creator.

"What kind of character" is an artistic question, that's solved out of the mechanics in the highest level of abstraction.

"What kind of game" is part creative and part mechanical, mostly related to the general aspect of the game genre.

"What options do the character have" is mainly mechanical and quite specific. Solving this is the hardest problem from the second-layer game engine perspective, and requires adding mechanics features ad infinitum. The time spend can be compressed with a language of mechanics though.

If you consider all the different species on Earth, two sexes are by far the most common. I once read there is a theorem stating two sexes is the optimal number of sexes because three or more sexes are not a stable condition (one or more sexes disappears after some time). And one sex provides less genetic variation if I remember correctly. If we will ever be able to see an alien there is a strong probability there will be two sexes of them.

Sexes are in my opinion important and you should have them in your character customization system. If you really want to provide more sex options you can give the opportunity to create new sexes.