I'd honestly doubt they did it because "lulz no gurlz alowd", really, it was more a thing of "oh well nobody needs this, we can trim it to save space/time/etc, somehow ignoring the fact that in English, pronouns are gendered whereas they aren't nearly as much in Japanese. The original script likely never made mention to player gender, meaning the most probable situation was just a translator snafu - more of a "didn't think" than "thinked wrong".

I know they've gotten SOME complaints, but considering how many people were flat-out mad that Gates wasn't Explorers of Sky, I don't know if it got the attention it should've.