This is a contradiction.
This is the 14th main entry in a Japanese game series that premiered on Japanese consoles, had 12 of the 14 originally exclusive to Japanese consoles (later ports don't count) originally created by Japanese creators in a Japanese company located in Japan for a Japanese audience.
This 14 entry is staffed by Japanese people. The artists and designers are Japanese. Most of the writers are Japanese.
The fact that they've embraced the fact that foreigners actually LIKE Final Fantasy and made the game accessible across many nations doesn't change the simple fact that it comes from Japanese heads and Japanese hands, thus making the game Japanese.
Moreover, something incredibly nuanced like this that IS considered a problem (specifically, a joke) in their home country (where their Japanese bosses and Japanese stockholders live and can tell them, in Japanese, that it makes them uncomfortable) but evokes feelings of "betrayal" from a very select group of foreigners (and an even more select group of their own countrymen and women), it behooves them to do nothing and say nothing, both by their culture and basic Public Relations logic. Therefore, they take the safe route that only gets them actively ostracized by a very small subset of players.
And then you consider that there are foreigners who hate the idea of men in dresses too, and you have a whole hornets nest it's best to just avoid entirely. You can't please everyone. It's actually an interesting Japanese frustration with foreigners too, since we come from wildly different backgrounds even within the same country.
They made their decision, and yeah people are going to criticize it and that's their right, but it's very important to remember that this isn't as black-and-white an issue as people are making it out to be, and that you're dealing with the interactions and differences of dozens of cultures.
Yes, in some cultures and for some people it's considered "unseemly" for a woman to dress in men's clothing (and was for many years in the U.S. even.) but for many reasons this has successfully changed. The reverse hasn't become as accepted.
Though my theory is the cultural allowances for women in men's clothing can have a lot to do with men's clothing being a lot more practical than women's clothing in many cases.
Oddly enough I do NOT think the problem is Yoshida, but possibly someone in the art department drawing a hard line, or someone above his head, because his wardrobe we've seen includes scarves, shirts with cuts usually seen in women's clothes, etc. Not totally "feminine" but not the western idea of traditionally masculine either. And as mentioned there have been a lot of outfits that skirt the line of masculinity and femininity.
But we don't know the whole reason, and we'll probably never know the full reason because stating as such would be a PR nightmare and create more questions than it would answer. Mostly because there's no answer they can possible give that wouldn't make people more angry than they actually are.
"More freedom" is a good thing, but sometimes you have to weigh the costs of that freedom.