Customers are stored in Craft Commerce for the purpose of having a single place to relate orders to. A customer will always be created during checkout if they are a guest, or if the user is logged in, the customer related to the logged in user will be used.
Logged in users can only be a single Customer in the system. A person may checkout as a guest customer with the same email multiple times, and a new guest customer will be created each time.
When a user is registered and verified, all orders for the email address belonging to that user are transferred to them.