When you registered your application under App Registrations, gave it permissions to the API and then performed the consent to those permissions...it automatically creates the registration in Enterprise Applications. Basically, the registration under Enterprise Applications is the instance of the app for that directory (tenant). If the app was multi-tenant, it would also need to be registered in Enterprise Applications in the other tenants needing to access the application. If you remove the registration from under Enterprise Applications it will remove access to the app for that tenant. In order for users in that tenant to regain access to the application, the app would need to be re-registered under Enterprise Applications and the consent would have to happen again.