I know I shouldn't but I want to configure it to use at least a different small folder in my system, any way how?
Unfortunately there's no way to do that, the game is hard coded to use its own folder. This was intentional to protect your files since the file manager I built could have bugs in it, and the 2nd update actually fixes one where you could corrupt your files by copying them.
You can do the opposite though: Copy your folder into GodotOS' files and work with it from there.