With the release of the server-script folder many new modding opportunities have opened up for user hosted servers. Some of these spill over into Uber servers, some do not. In this thread post the results of your experimentation with server scripts on uber servers. Confirmed Not - Setting custom color table.
But... @burntcustard set up a custom colour table? Edit: Or well- you said Uber's servers, so nevermind I suppose.
I believe that all of the scripts are loaded on startup. I haven't tested whether host mods are visible to the require mechanism, but the vanilla server doesn't load anything after mounting mod files.
That's done via an explicit file load of the JSON at an appropriate time - so file.load at least does respect shadowed files.