vim-zettel VS md.obsidian.Obsidian

Maybe the vim-zettel? https://github.com/mattfair/vim-zettel

My Flatpak version was updated the same day. Very impressive.

I tried flatpak command line instructions as mentioned here but that too giving error

There are Linux solutions to this, macOS makes apps request permissions to important folders/ full disk access, any operating system should let you run something as a locked-down user without read/write access to your important files, etc. Installing Obsidian on Linux using flatpak or recent macOS + a firewall would let you manage a lot of the risks there, for example.

If you want simple markdown notes I recommend Paper, for to-do lists a good option is Endeavour, and there is third option, Obsidian, I don't use it because it feels complex, but maybe you will like it

Is that not this? https://flathub.org/apps/details/md.obsidian.Obsidian

It's probably best to open an issue here to ask what's going on if you're interested: https://github.com/flathub/md.obsidian.Obsidian/issues

You can check in github repo how a flatpak package is done. Here is how Obsidian is done. If you don't like any permission, you change it through flatseal app or command line. Most gnome apps and apps that follows gnome HIG are maintained by the official developers themselves. Valve, Mozilla are maintaining their respective products.