DoodlesEpic/JoplinDesktopFlathub

This flatpak only have permission to access user's home directory.
Need to manually add permission to allow access other location.

You can do it with Flatseal, and configure permissions with nice gui.
Or use terminal command:

flatpak override --filesystem=host net.cozic.joplin_desktop

Note: You can also use multiple filesystem options to set /media,/run/media,/mnt as you need.

There are two ways.

Nothing need to be done, it's done by electron.
Joplin will open a dialogue to select editor.

• How to reset the xdg-open choice
  flatpak permission-remove desktop-used-apps text/markdown net.cozic.joplin_desktop

This can run command outside flatpak, which means this flatpak most likely to be unsandboxed.
This feature is enabled for full external editor support.

Path:
/bin/flatpak-spawn
Arguments:
--host <outside command>

Path: 
/bin/flatpak-spawn
Arguments: 
# run flatpak app
--host /bin/flatpak run --filesystem=xdg-config/joplin-desktop org.gnome.gedit

# run native app
--host /bin/gedit