Nah, that was a pretty dumb debate about a made-up character.

Cortana is not a female. She is an AI.
She chose to look like a naked woman (likely a younger Halsey).
Why? Because that was the AI's chosen form, and it's Not A Big Deal™.
She doesn't have lady bits because she's not a human, she's a hologram, and it's Not A Big Deal™
There have been times when her code gives the appearance of clothing, but as you acknowledged, it's not real. It's code.

: Cortana's chosen appearance has always been one of 'ideal female form', for
: empowerment or gaining the upper hand through discomfort (I believe
: there's a quote about that somewhere)

Yes, that was the 343-patented BS-Excuse-To-Try-To-Give-Everything-An-Explanation-And-Leave-Nothing-To-Mystery. I think it was what started the entire sad debate about her being naked all these years, which 343 decided to retroactively change to suit the really awkward "what old white men think women would like, while not making themselves uncomfortable" direction that Halo has gone in.