Don't use the portals for this level of access. I can tell the XDG portals are being used because that's why you're getting the path beggining with /run.
If you're using the Snap, run:
sudo snap connect joplin-desktop:removable-media
If you're using the Flatpak, run:
flatpak override --filesystem=host net.cozic.joplin_desktop
Both of these will give Joplin direct access to the folder in /media with a lot less technical traps involved.