I should clarify that I don't think it's because it's because Japan is amazingly progressive about gender. (After all, this is the game where he gets groped by :biden-troll: who exclaims "You're... a man?!)
It's just that Japanese character designers can go "I think the dudes can and should be pretty too"
I think Kojima and Kompany do a great job of subverting and elevating expectations of their playerbase on a regular basis. From the Snake Eater, to the P.T. demo, to the Death Stranding, all of them have Kojima and Krew doing shit that make players feel something. Good or bad, I think it's a designers job to make players feel something.