Okay so I personaly don't play as a female character, but when I was thinking about doing the main quest or not because my character was an argonian and I was thinking if that made sense or not, I suddenly began to wonder how the nerevarine would work if he were incarnated as a woman?

I'm not seeing the problem. Why couldn't the Nerevarine be female? There are philosophical traditions that believe we can reincarnate as animals and plants.

This, of course, assumes that our characters actually are the reincarnation of Nerevar. Perhaps they are not. Who knows?

It works exactly the same. Except people say "she" instead of "he."