Sorry, can you explain a bit more? What other things? This mod does not actually look at the folders at all; it grabs the stuff from the Kobo's own database so it depends on what your database looks like. I've already excluded some entry types as otherwise it would create collections without any content.
https://github.com/frostschutz/Kobo/...toshelf.sh#L49
You could change the condition there to file:///mnt/%/Books/%
https://github.com/frostschutz/Kobo/...toshelf.sh#L59
And change this to (onboard|sd)/Books/
Putting that in the official mod would require everyone to move their books there and re-index the entire database; I guess I'll have to introduce a configuration file or something for such things.
(I guess I'm not the only one who doesn't have everything in Books/?)
Edit: Also you can put anything you don't want in the database into a .hidden dir that starts with a .