I wouldn't have minded a technical explanation at all, to be totally honest.
Edit 1st of January 2018: I noticed Mood Rock quoted this post in the New Years post so I've decided to clean it up a bit and clarify my points.
This is pure speculation but if I had to guess, it could be a result of any of the following:
1) A glitch in ambient occlusion. The game renders shadows with a wide assortment of colors (see below), and this game is full of broken meshes, so there is the possibility that the game is casting shadow upon shadow on itself resulting in these deep hues we know and love.
2) Out of whack vertex coloring. This is a technical one. To my understanding the game uses vertex shading to choose how to apply per vertex (Gouraud), if not per polygon shading. Open some of the models with pview if you want to see for yourself. The jails are particularly colorful because they wanted to add atmosphere. I'm thinking someone might have colored in the rock as practice/fun and that version got pushed to the live servers.
3) Extra information added to the model. This project is rebuilding the game from all that they could find in the phase files so there is the possibility that extra information was added to the Port Royal model to make it work. Panda3D makes no distinction between large or small models, between an island or a ring on your finger. Islands just happen to be bigger and harder to work with, and include collision information.
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Shadows tend to be colored red or green, and subtractive color mixing gives us just about all of the colors that have been seen on the mood rock. (I don't know how cyan works into this so I'm a little iffy here. It could be any number of things.) I have access to an old version of the phase files but I don't fully understand how this game processes light yet.
If a developer who knows the truth wants to chime in please feel free to revive this thread anytime. Anyone who wants to examine the files for themselves may find a copy of POTCO (not up to date with TLOPO, but just as useful) phase files here:
http://www.mediafire.com/file/um393br70u0576v/POTCO+Phase+Files.rar