@MazikeenX only thing I can tell you is that it's using the exe files in %localappdata%\Plutonium\bin with the exes in %localappdata%\Plutonium\games as an argument. Don't know how it works exactly or if it has other arguments but maybe this will help you.
If you're using a game launcher like GOG Galaxy then you could either launch plutonium.exe instead of the game directly or create a macro that starts the launcher and click on Play or wait for an answer from staff.