Just looked into this issue again with a fresh mind. I think it's not solvable without support in the platform to backup directories outside of /app/data (or alternately, we have to install dokuwiki in /app/data )
The last update explicitly removed the admin status propagation from Cloudron user accounts to the app. This is done to unify how user accounts get permissions assigned within all apps. The idea is, that the Cloudron admin status is not carried over to apps, since apps have too many different concepts what an admin is and is not.
I guess there is no good way without requiring manual permission changes to move to this new understanding what admin means on Cloudron.