If you take a look at the screenshots I posted earlier you will see that in an editor/photoshop it looks fine, but once in game the texture doesn't actually cover the entire model. It looks to me like it is using the textures almost as lighting, wherever the model would be seen up close/in light, the textures load, presumably because those are the only times you would need to see details, especially for a game seen from the top down and pretty far away. Even if, for example, you were to just make links textures a flat black color, that color would only be seen when you are up close, and even then it would not cover the whole model. This is the case for both TH and ALBW, so something else is giving him a green color on his tunic, or yellow hair. I still really think it could be some sort of shader, as there are some shader files for both games, but on the other hand it could work the same way as Smash Wii U's models and simply be an overlay on a model that just has the geometry in flat colors.