I figured it out, it was the storage configuration. I always use host mounted path for storage for my apps, and when creating the datasets I select the Apps ACL for it. That has worked well so far but doesn’t for Joplin. Selecting iX volume instead worked, but I want to use host path.
In the iX volume installation I saw in the logs that the app checks and sets modify permission for user 999 (netdata), but adding that user to the ACL didn’t help. Do you know what permissions are required to make this work?
Edit: Explicitly setting netdata as owner using chown seemed to do the trick. This should probably be handled or at least mentioned in the installer when using host path.