With an Enterprise Developer License (around 300$) you cannot distribute through the Apple Store. Distribution can be through MDM (Mobile Device Management) or OTA (over the air). To my knowledge the provisioning file needs to be updated each year. Advantage: there is no control of Apple because you distribute directly BUT you are only allowed to serve phones within your company.
If I'm not wrong, its' the company that have to subscribe to the enterpise program, then the company enable you as developer.
So the enrollment must apply to each company you develope for.