You can set the color of your ships when you start a game by customizing your race. This isn't a "mod" since it's part of the core game functionality. Mods are things that alter how the game plays, such as rules changes, adding in tech, weapons, ship models you created outside of the game etc...
The UI is also designed to be moddable, and I think you'll be able to modify that as much as you like without it affecting the metaverse status.