Instead of having users modify the config.edn file, have a user-config.edn file that supersedes the defaults. This way any updates or changes to config.edn will automatically be made when Logseq is updated without the user needing to occasionally download a new config.edn file and copying over previous changes.
@Luhmann Agree this workflow could be improved. A workaround until we have something in the app is to look at the latest commits in the authoritative config.edn - History for templates/config.edn - logseq/logseq · GitHub
@cannibalox has some other interesting solutions to this workflow too