I do have some sort of the same issue... I passthrough a HBA with 8 drives for my TrueNas vm runnning on Proxmox.
I did the TrueNas installation, then I passthrough the HBA card with my 8 disks attached (since it is a passthrough this controller / disk don't show up in (VM -> Options -> Boot Order) but now when I boot, the vm try to boot from the HBA disk instead of the VM os disk... any idea on how to change that permanently ? Pressing esc does not seems to work for me. the system try to boot from the hba and then detect probably the zfs data partition because I get : "This is a FreeNAS data disk and can not boot system. System halted."
If I press Esc at boot I can get the Boot device menu but I can't the Virtio-scsi Drive as default