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.
Never owned a Surface, so can’t comment on that, but I’m very happy with my One by Wacom (not to mix with Wacom One :p). It’s fairly cheap as far as these types of tablets go, it’s very responsive (I have 144Hz displays and it’s so nice to use), has a nice sueface roughness, it’s plug-and-play on Linux and has 0 maintenance (no batteries to swap).
What I like with my setup is that, contrary to traditional writing on paper, I can sit properly, looking forward, avoiding some bad neck and back pain I usually get otherwise.