One question - flatpak still asks me to choose, if I want to save a new app into system or user. I recently installed OCR Feeder this way, but am not able to save any document produced with this app. Is this maybe connected to those flatpak issues and if yes - how can I change this?
Thanks!
Likely an upstream flatpak issue.
Each flatpak has a list of allowed resources. These can be ~/Documents, ~/Videos etc. or device nodes that it needs access to. If the application isn’t properly configured with access to these resources, it can only write into the flatpak sandbox, and then you won’t be able to do much - maybe you can write into the data storage, but it’ll be difficult to find. I suggest checking the bug tracker for the OCR feeder program on github.com/flathub and seeing if it’s listed.