Every WP download has multisite capability, whether it's activated or not is decided in the installation process. Your question piqued my curiosity so I took a deeper look. Most of the related functions are in wp-includes/mu-functions.php.
I am less convinced now that somehow porting the multisite capability to single site is practical, but it could be used as a model for a custom implementation. New registrations are stored in a table separate from the users table. This makes sense, the volume of registrations, especially those never verified, can be quite high. It would be more efficient finding such registrations and deleting them when all data needed is in the same table. Using the users and usermeta table would be less desirable.
When a user registers, their data is stored in this table along with a datestamp and activation key. The key is included in the verification email activation link. If the user follows the link, the key is verified and if successful the user is added as an actual user.
I did not find the relevant code, but presumably there is a scheduled event that runs on occasion and deletes any old registration entries that were never verified.