It's not a masculine pronoun. Look at how grammar functions in some sentences: 'if anyone needs a copy, he can get one here'. Obviously 'anyone' is not masculine, but it is singular so you can't say 'they', you have to say 'he' (or 'she', if it was something like a Women's Rights convention). So in this case 'he' is gender-neutral.
As for God, it would seem that He is literally the 'Father', but the truth is, He is gender-neutral as well.