Hyde here from Shopify. Interesting question!
When you receive the error message "A store with that domain name already exists" it suggests that you may have connected that domain to a different Shopify store previously.
You could have created that store in error, or simply have forgotten that you created it. I would recommend having a search for details of that old store in your email inbox. You could also try inputting your different emails in this recovery form to see if you can recover the store in question.
Failing that, you could contact our support for help in finding the domain in our system in order to find the store it is linked to.
I hope this helps!
All the best, Hyde.