I am new to this myself, and may be mistaken in many respects, but my understanding of the 'Organizational Accounts' / 'On-Premises Authority' option for MVC apps is that it applies when you've set up Active Directory Federation Services / Windows Identity Foundation.
The primary motivator for doing that would be if you want to allow single sign on to cloud based apps based on your internal AD, or allow certain types of SharePoint SSO integrations with custom code. If you're not looking to do a cloud service + internal services seamless blending of authentication, then just choosing 'Windows Authentication' would be the far easier way to proceed.
If you do want to proceed with the WIF / ADFS approach, then the following might help:
Hope I'm not leading you on a wild duck chase with this info, but for the moment, that appears to me to be the most applicable information I could find.