You are installing packages from /boot/packages/ - tcl, expect, openvpn. I'd recommend finding another way to do this. Use the nerd pack for packages, and a docker for openvpn. These packages may be holding up a shutdown.
EDIT: Also check this error:
Fix Common Problems: Error: Docker application binhex-deluge has volumes being passed that are mounted by Unassigned Devices, but they are not mounted with the slave option