Well see I'm speaking from and in universe perspective, not specifically design reasons. The reason the chief is a big dude with a cool voice and Cortana is a naked computer program is simple, it appealed to their consumer base. As for the other examples, tbh idk, if Bungie published a design doc for Sgt. Johnson and Dr. Halsey I'd be interested in reading it though.

Lorewise, the chief being a big dude makes sense, genetic mutation and all. But there is, imo, no real convincing reason why Cortana needs to be as she is, or why Halsey would design her like that. While it is true as you say Bungie didn't make put much effort into making Cortana have sex appeal beyond her model, we kind of already discussed that with her being on the lesser end of sexualization compared to contemporary games at the time.