Kojima was hardly coy about Quiet being sexy (I mean, come on, he distributed high resolution images specifically to assist cosplayers so I think his intentions were clear) but honestly people are pretty dedicated to thinking that the 'reason' for her outfit is the in-universe explanation that Ocelot gives. There is a storytelling reason: Quiet is a woman that is silenced, turns invisible, will literally die if she puts on clothing, has enormously remarkable abilities and is highly capable, but is widely feared and despised, considered untrustworthy. It amounts to a view on how men view video game heroines - Kojima isn't subtle.
You can talk about the effectiveness of that commentary or the necessity of its components, but he wasn't
pretending. The guy's career includes Meryl in her underwear and pin-ups on walls and dreamscape photoshoots with real world models in painted-on jumpsuits among other pieces of deliberate fanservice. If that's all his intention was he wouldn't have bothered with some kind of false justification, he would have just done it.
Anyway, 2B is just good looking and wears an attractive dress so I'm not totally fussed about why Taro did anything in particular, but just throwing it out there, the guy behind Dead or Alive said basically the same thing about his female characters and he's generally thought of as a creep. Maybe it has more to do with liking what the guy is selling rather than any kind of general principle