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"
Also from a design perspective Raiden appears androgynous to play up the fact that he's the avatar for the player, regardless of their gender.
I guess the reason Raiden has always stood out in particular is that while MGS is a very Japanese franchise, since it has many of the trappings Westerners like (scifi military fiction, guns, shooting dudes), it's always had a broader audience than something like a JRPG. In other words, dudes who like regular shootybang stuff also played MGS and weren't prepared for the bishounen protagonist
and then they lampooned it in MGS3 by having snake wear a bishounen face mask
They further dumped on Raiden in the form of Raikov. I never minded Raiden so both making fun of him in 3 and "fixing" him in 4 seemed unnecessary to me