Earlier quoted context omitted.
If you're using a flatpak, that's not actually the case. It would have very restricted access to the point where you even would have to explicitly give it access to user /home.
You're wrong. The obsidian flatpak ships by default with access to /home. https://github.com/flathub/md.obsidian.Obsidian/blob/5e594a4...
The first time I started installing flatpaks I ran into a bit of permission / device isolation trouble and ever since then, I use flatseal after installing an app to make sure it actually has access to things.
I guess I misremembered in the case of Obsidian.