I believe minimising is disabled on linux entirely so the option won't do anything regardless of what you set. Something to do with the tray on GNOME not playing nicely I think?
So, I pondered a bit and thought that maybe I could get the behaviour I wanted by just killing the Joplin window straight after auto-starting it in my config, and after some searching I cobbled together this, which worked!
#Autostart Joplin.Appimage
exec --no-startup-id /opt/appimages/Joplin.AppImage
# Then shut Joplin window, leaving it running in Tray
exec --no-startup-id i3-msg '[class="Joplin"] kill'