This guide worked great until I did an update on to the sys-vpn-protonvpn-app standalone qube on 9/27/2025 and then it quit auto-starting on boot. I did some probing around and found that after the update . desktop file had changed from protonvpn-app.desktop to proton.vpn.app.gtk.desktop. After I put a copy of proton.vpn.app.gtk.desktop into the ~/.config/autostart every thing would auto-start on boot same as before the update.
qubes 4.2.4
I hope this info is useful.