configure URLs in system workflow messages
It's entirely possible the stock template doesn't account for this. There are some cryptic parameters you can add to crmURL to force a frontend or backend url, respectively: fe=1 or fb=1. (That's not a typo - fe=frontend, fb=forceBackend)
I don't use joomla but if that works for you can you either make a lab ticket at https://lab.civicrm.org/dev/joomla/-/issues/new or if you can make a PR against core.