ATM, you can save config overrides, remaps and shaders in three different ways. Either save a core overrinde, a dir override and a game override. These cover all possible scenarios you want so you can separate configs.
However, core options (the .opt files) can only be saved per core (by choosing the new option to have those in the config folder instead of the root) or per game (by going to the options and saving for the game you have loaded). It all handles differently than config/remap/shader overrides though and there is no way to save .opt files per dir.
Could this be implemented?