Microsoft For iOS App protection policies

When the apps are downloaded from Company portal, then Intune recognizes them as managed and they fall under the managed channel. If the apps were installed outside the company portal, then Intune will recognize them as unmanaged. For APP to work on managed devices, use IntuneMAMUPN key in the App configuration. Also, things will depend on how have you setup the APP. If you are using managed app filters, then the assignment can be different. If not and you have targeted a user group only, then APP should apply on both managed and unmanaged apps.