My solution would be:
- Ruleset comes with a list of "if a moron installs this, this is what they need" config stuff in it.
- This changes the default values of these options whenever that mod is active.
- Upon a new activation of the mod (from the mod page, not when starting the game and looking in the config to see what mods should be loaded on startup), it also changes the active values to the defaults.
Nothing is enforced, but when starting to use a new mod, the "reboot the game to load mod" also sets the active options to what is needed. This makes a complete transition from [ vanilla with vanilla background and vanilla config ] to [ Piratez with Piratez homescreen and Piratez config ]. If the user then reviews those options, and decides that, no, Extender is crap and they don't want to use it, then they can turn it OFF. And next time they start the game, it will still be OFF because it's not a fresh start. But it was ON at the start, like it should be and ensuring that most users use the mod as intended.
Then video, audio, keybindings, debug mode (which has caused issues in the past when the config had it active and suddenly people couldn't quick save/load) and other such options can be left entirely for the user to decide on.
This is how I would do it. But honestly, I just go fish the mod from the user/mods folder of the zip file and put that into my install of OXCE+ (which runs both XPiratez and XComFiles by swapping data, user and config directories), so this is academic. Since I don't want the great (striving and arguing about what's the best way to do things) becoming the enemy of the good (doing something better than shipping configs), that's my last post on this.