The issue is fixed since unraid Version 6.10.0 2022-05-07, so you only need to use the script on older versions.
So the fix I'm using now (tested on Unraid 6.8.3, 6.9.1, 6.9.2) is to edit /etc/rc.d/rc.libvirt ->stop_running_machines to correctly handle paused VMs on shutdown/reboot or array stop. Basically I just added commands so stop_running_machines tries to resume the paused VMs, after that they will be hibernated/shutdown as usual.
rc.libvirt is not persistent so I created a php script to edit it as needed, I'm running the script with CA User Scripts with the scheduling set as "At First Array Start Only" (need to run the script once after creating it). php script file attached
