That is expected (and documented) behavior. There are some components of the system that do not support user@domain.tld usernames, and so there have to be two names in order to actually process and deliver and receive mail with that username.
There is no harm in having two users; Virtualmin will manage the passwords and other facets of the users for you automatically, so you don’t need to think about the multiple users. It should be mostly transparent to your users; only root and administrative users will see the additional users, and users should be able to login with either username.