You can use the AuthAliasOnly directive to control how and where real usernames get authenticated (as opposed to aliased names, via the UserAlias directive). Note that it is still impossible to have two identical aliased names login to different anonymous sites; for that you would need <VirtualHost>.
Example: ... <Anonymous ~jrluser> User jrluser Group jrluser UserAlias ftp jrluser UserAlias anonymous jrluser AuthAliasOnly on ... </Anonymous>
Here, the <Anonymous> configuration for ~jrluser is set to allow alias authentication only. Thus, if a client attempts to authenticate as 'jrluser', the anonymous config will be ignored and the client will be authenticated as if they were a normal user (typically resulting in `jrluser' logging in normally). However, if the client uses the aliased username `ftp' or `anonymous', the anonymous block is applied.