This is about the two settings "Include domain name in usernames" and "Domain name style in username" from "System Settings / Virtualmin Configuration / Default for new domains".
Changes made to the former of those settings are immediately applied, also to existing domains. The latter though seems to be applied only to really new domains. As in, when I change it, and create a new email user in an existing domain, the change is not applied.
For one, this appears to be a somewhat confusing inconsistency in terms of when those settings are applied, and then, I'm just now trying to figure out how I can change the latter of those settings for existing domains, in case I change my mind and would like new email users for an existing domain be named "user.domainpart" instead of "user%domainpart".