hmm... indeed that particular scenario would get broken.
About C:\Program Files\WindowsApps get a VM and try it for yourself, you will be surprised how nasty windows is with regard to some of the sub-folders in this location.
iirc. with System/TrustedInstaller permissions you at least can create new files but no chance modifying existing once.
I think windows 10 is using here some additional flags/attributes to protect these locations.
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