She has the personality of a woman, and she has a female voice.
To say she is not female is like saying Labrys, Android 18, EDI and Aegis are not female.
What the hell is a personality of a women? XD Yes she has a female voice and? Imagine she is just a male Robot who likes to have a female voice? Ellie on the other hand has a ton of emotions, the feels absolutely real and that is not only because she is voiced by a great Ashley Johnson but also because she is a great maybe even the best written Female Character this Industry has.
Videogame characters are all "robots."