To make launcher a system app, please add the attribute android:sharedUserId="android.uid.system" to the <manifest> tag in AndroidManifest.xml file.
If you have a Premium license, we have a special build variant for Headwind MDM launcher signed with the firmware (platform) keys. Please contact the support to get it.
I am pretty sure that Headwind MDM launcher signed with the firmware keys and using the android.uid.system shared user, will run shell commands as expected.