iOS Company Portal Security

No security protection would be applied to the application (MDM restrictions would apply across the device), you would be relying on conditional access to enforce a level of control at the application sign-in/authentication level to ensure the device is compliant etc. (if in place and if the app uses SSO).

Data stored from the application would technically be unsecure as there's no security controls applied. You could request management of the app, which would allow Intune to block Icloud backup, removal during unenrollment etc. 

Managed applications would NOT be able to transfer data to the unmanaged application (unless MAM is updated with an exception for said app). In this case, your app would be considered unmanaged and would not have the restrictions applied - allowing the application to export is data to the device, over bluetooth etc.