Regarding the "biovestite" line, the word that Kojima used was バイオハーフ (bio half), which was almost certainly inspired by the Japanese word ニューハーフ (new half). In Japanese, "half" was commonly used when referring to individuals who are half Japanese, half another ethnicity. So one would say so-and-so is a Japanese-American "half." It's similar to saying one is "half Japanese, half American." Since the game was released, it has generally come into view that the term has a discriminatory tone ("half a person"), and alternatives like "mixed" are preferred. Japanese has a tendency of taking English words and re-purposing them (wasei-eigo), often with totally different meanings from the original words. Japanese people do not realize these terms are sometimes offensive in English. The more globally conscious ones will, but not all. In time, awareness may increase, as it did with "half."
The term "new half" came about in the 80s. It's not clear who coined it, but it caught on when a pre-op transsexual, Rumiko Matsubara, entered a female modeling competition and won, later revealing she had been born a man. Therefore, a "new half" is a person who is, well, a new kind of "half." As derogatory as that term may sound to a native English speaker, again, this is wasei-eigo
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The "so-called women," however, that was not explicitly in the original Japanese. I added that because I saw it as appropriate, given Jonathan's extreme character (verbally and physically harassing nearly every woman he meets), my interpretation of "bio half" and the strip bar, and, as you point out, this nostalgia we see throughout the game. I couldn't imagine Jonathan not saying that in that situation, considering those three factors. So I am fully responsible for that line. But I don't consider it as going against the spirit of the game any more than the addition of the phone sex line conversation to the Sega CD version of Snatcher goes against its. It's just that Snatcher has a more playful tone, whereas Policenauts' is more 意地悪 (ijiwaru, "mean").