It has nothing to do with the capabilities of the AI. The characters were originally designed as such - with a dick and no pussy. Only because it suits the developers' tastes.
As you mentioned, on Itch this is the type of body structure most often meant by futunari, and it is the “default” for us. Because “futunari” as a hentai genre is a broader concept than the medical term “hermaphrodite”.
Also, HRT, pre-op and other medical terms have nothing in common with in-game fantasy universe, as characters there just born like this.