We could talk about storing Xposed Installer's settings, but a) there aren't many of them and b) in more and more ROMs, apps can only write to one specific folder on the SD card, which is deleted when you uninstall the app.
Backing up modules (which are simply applications) or even their settings is out of scope for me. There are many apps for that, e.g. Titanium Backup.
Tired of updating your mod for every new ROM release?
You want give users the possibility to combine different mods without creating tons of different files for all possible combinations?
Then have a look at my Xposed framework
- modifications without APK changes!