I have a "rare" mod which I acquired while farming the mod challenges. It started out gold. I have another mod, of the same type, which I found in a mod battle. It started out white.
After leveling them both to fifteen, the white one has turned out better.
The same thing has happened with two of my health mods, sort of. I have a three star health mod that is better than most of my five star health mods.
Since it's random chance whether or not each ability increases when you level them up, the colour only indicates how much potential each mod has and not the overall quality of said mod.