I gave this a shot today and it did a pretty good job except as per the following:
https://support.microsoft.com/en-us/kb/2798317It did give "ALL APPLICATION PACKAGES" group in:
C:\Windows [Read, Read and Execute, List folder Contents permissions]
C:\Program Files [Read, Read and Execute, List folder Contents permissions]
However, it did not give C:\Program Files\WindowsApps [Read, Read and Execute, List folder Contents permissions]
it didn't process all the directories under C:\Users except for the Default User folders and the current user folder which is supposed to give "All Application Packages" group Full Control permissions.
C:\Program Files\WindowsApps needs ALL APPLICATION PACKAGES to run the modern default apps or else the apps will just immediately close.