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That's right, Microsoft lock down those WindowsApp folders pretty hard. This affects all apps and games there, not just CK3. There are ways through it if you google enough!
 
I Googled for 2 hours. Literally. But only I got was access to game folder root itself, but not to it's subfolders like "game". I am not basic user. I am programmer with 15 years of experience and was not able to do it.

I think placing these "game" subdirectory somewhere on GIT or something just for modding can be good for modding community.