I may be confusing the two concepts but if you want to be able to remotely manage the app configuration with EMM it would need to either reference an external config file that you could also distribute to the devices or support Managed Configurations. To leverage Managed Configurations, both the app would have to be written to support them and you'd have to distribute the app to AE managed devices via an App Catalog rule and not a Package. My understanding is that the SharedPreferences approach would require either the APK to be recompiled with the specific value or manual intervention would be required to manually configure that value within the app itself if that is exposed.