You're wrong. The obsidian flatpak ships by default with access to /home.
https://github.com/flathub/md.obsidian.Obsidian/blob/5e594a4...
[1] https://docs.docker.com/desktop/settings-and-maintenance/set...
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.