Y'know, there was actually a pretty good analysis on /t/ (unheard of, I know. It was like one of the only salvageable posts on there) regarding some of the Peruvian imagery. Genuinely recommend going through it. A number of designs were directly pulled from Paracas textiles, most of which are directly symbolic of dreams and the mythology surrounding dreams in Paracas culture. I'm surprised nobody else has brought this up ever, but Madotsuki's sweater design looks strikingly similar to these military tunics worn by officers of the Sapa Incan military.
Among those, there are also various Japanese cultural references that I'm a little too tired to list off but most should be obvious if you've already gone through the game.
The reason why the discussion of this game is so limited (besides being old) is that everyone has a bad habit of trying to make massive stretches when discussing the game's imagery which lead to very personal, emotionally-charged and often very amateurish interpretations. When you only make interpretations that are nothing of worth, then I guess it's better not to discuss it seriously at all. That's why I find a lot of stuff like this riveting and I think it's depressing that this game's had little to no proper analysis done in the time it's been out.