Some apps like Obsidian needs permission to access every file on the device. It is surprising Obsidian isn't getting called out on that very much.
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According to Exodus it has no trackers and it's an open source app also so you can see what it does (though tbh I didn't check that for the mobile one)
If there's apps to call out there's way worse than Obsidian.
Surely Obsidian do not to see all files on the device, it only really needs to see the files the user needs it to see.
On FreeBSD I can build a full copy from source (in fact I have to, there is no binary package). The only issue seems to be licensing, not source availability. Personally I don't care about licensing (I completely ignore it all anyway) and it doesn't stop you from inspecting the source code.
I think Obsidian is a really great package, I just happened to have moved over from OneNote which is horrible Microsoft mediocrity and doesn't even have a Linux app. And the web version is really useless, it needs to refresh every day and it can only search within the same tab, not a whole notebook. Such a mess. Obsidian is so quick and efficient <3 And there is full self-hosted syncing available, which I also use.
May be the freebsd build is using some binary library packages?
A cursory search indicates that one of the freebsd 'build-scripts' used for installing obsidian uses a binary package for obsidian itself, not building it from source.
It strange that about obsidian which seems to be rather popular here has many people thinking that it is open source, when it is not.
That's just a user contributed thing though. It's also just in the official ports collection. There's only a makefile there and some config files for electron (electron is kinda a PITA to compile on FreeBSD because there's no package)
Now, it can update itself automatically but it's all JavaScript. No binaries.
But it's safe enough for me anyway. Especially because the dev community uses it do much. If it did something untoward it would be noticed quickly.