Hello,
I also have kind of a similar problem on Arch with i3. I use the same command and when the PC starts both window and system tray icon pop up. What I would expect is for only the system tray icon to pop up, without the window opening. It's rather annoying and I haven't found a workaround yet.
Would be glad if there was some information on this problem.
Edit: I tinkered a little bit and found this simple workaround:
exec --no-startup-id i3-msg 'exec /opt/Enpass/bin/runenpass.sh'; sleep 0.5s; i3-msg '[class="Enpass"] kill'
It's not perfect but it works until this issue is solved. Also you might need to edit the sleep duration if it doesn't work for you.