But I still have a little thing I wonder about. In MacOS I store settings files in the Application Support folder. Within that folder I create a sub-folder with the name of the Bundle Identifier of my app. In there, I store my several files like a SQLite file for my settings and some email templates. Stuff like that. This way it is all bundled together.
Is it common to use these sub-folders in Linux as well?
In the Linux world there is a lot of flux regarding application-specific folders. There is this page:
Regarding to this standard, you should store app specific state files in /var/lib/_appname_.
However, the latest best practice is as per XDG Base Directory Specification is to use $XDG_CONFIG_HOME which - if not set - defaults to $HOME/.config. I would recommend that just because it is user-specific and easier for the user to backup these files.