Custom Biome Palettes specified in color.properties don't seem to work in Colormatic, but they work perfectly in Optifine.
This is an old MCPatcher feature that is documented here

I also made a resource pack to test it, white wool blocks should appear purple:
Optifine:

Colormatic:

Resource Pack:
Biome Palette Test.zip

Colormatic version: 3.1.2 for Minecraft 1.19
Optifine version: 1.18.2 HD U H7