Yeah, I might also need someone on Linux who has Amnesia installed for testing later. I have an Ubuntu VM, but not with the game.
Perhaps I might even need to buy a retail version just to make sure it works with it.
Anyway, it should be able to detect any main_init.cfg files in a specified folder. If you select the Amnesia root folder, it will find them regardless of location in there. Personally I'd prefer a /mods folder but it isn't strictly necessary. I did select my C:\ drive once, and it managed to sniff out 6 mods on it, though it did take like 4 minutes, so I don't recommend it
Besides, even if it finds mods outside the Amnesia directory, they won't run without the game itself.