[R&F] Question to Configuration and Mods

I had set up a configuration for Giant Earth with ca. 30 AI civs and ca. 30 CS and saved it. I then adjusted a mod for R&F and tested it in a normal game. When the mod was fine, I left it activated and returned to Giant Earth. I loaded the configuration and started a game ... and the mod was not active. I then started a normal game with Giant Earth and the mod was working ...

Is it possible, that a configuration contains a list of all mods which were activated when the configuration was saved and when a configuration is loaded, only those mods are used when a game is started? This would be really strange since the setup window for configurations does not list any mods and does not allow to add/remove mods.