They can register with the same email, but not the same username. They will have to choose another username. If you force email to be the username, they will not be able to use the same email.
What do you mean by select the home folder? Addon companies are for a SINGLE installation for Blesta, so the files are the same files. If you are doing a separate installation of Blesta (different copy of files), this is not an addon company and would violate the license. 1 license is for 1 install. Addon companies can be added under Settings > System > Companies. Your web server must point all the companies to the SAME docroot where your single Blesta install is located.