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What does Windows do? Genuine question, I’ve not used it since the 7 days. Regarding Linux, that’s true for stuff installed through regular package managers and whatnot, but Flatpak is pushing a more sandboxed and permission oriented system, akin to Android.
Yeah Xournal++ is probably the best hand-written note taking and PDF annotation program available on Linux, it’s pretty well known. The system settings permission is to honor some global settings you might have enabled, and the file system access is so you can save and open stuff from anywhere, I assume.