Why can't a god be female? Why can't the most powerful gods be female? Why can't the most ugly, least likeable gods be male?
Such things can be evidence of an agenda if they are employed along with other, more concrete things, but alone? No.
For example, if Magran started bitching about Skaen mansplaining something to her, or if Hylea started accusing the player of employing the male gaze while eyeing up a romance interest, or if Eder began self-flagellating on account of his white male privilege, or if Pallegina accused the player of being subconsciously racist upon not inviting her to the party...
If any of those things happened, then I might take another look at the sex of Deadfire's gods with a bit more suspicion.
But none of those things are in the game, so I have no reason to assume that Magran being female, for example, is motivated by an agenda, rather than it merely being chance, or something that fitted the character, or an aesthetic decision, or any number of perfectly fine creative choices taken by the developers.
Not that you genuinely care either way, since you're just a sad little troll trying to stir up trouble, rather than the barnstorming intellectual you probably think you are in your mind.