I went digging through some old sites and then used the Wayback Machine to find the original content of the sites (now lost) and then used Google Translate to translate the content into an approximation of English. Long winded, I know. But I couldn't find this information anywhere else.
This info is mainly from the Toyota Japan site, back in 2002-2004. And yes, the color coding is tricky and doesn't make much sense. I think they mean this:
■ Special Features (red)
■ Standard (blue)
■ Optional (yellow)
■ Dealer installed options (by Moderisuta) (purple)