The primary domain for each org consist of {orgname}.{instancename}.{tld}
But generally speaking this is only used as grouping container for users and suffix their usernames.
If you dislike that you can turnoff that each user is suffixed with this and allow them to use any name. OR you can verify domains on each Organization and then set them as primary for a specific org.
I.e i verified this domains on my org which gives my user multiple login names (yes i know my mail is in there, but thats already a spoiled address )