It depends 
When you do the import from HCM, the user ID is set to the user ID of the object. If you want to change it to set it to the mail attribute, you can change the process so that it selects that one. Which one you use can be controlled via the HCM query and via the create job.
If you're using another process to get / create users you'll need to provide more info so we can help.
Peter