I was able to solve the problem after finding this reddit thread titled "kvm_hba_passthrough_will_not_boot_form_virtual" (sorry, can't post link as new user) and the linked post on freenas forums.
TLDR, disable BIOS boot option in the HBA configuration
I'm installing FreeNAS on a VM with a 128GB boot disk (Virtio / ZFS zvol) with PCI passthrough to a LSI SAS 9207-8i with 4 disks attached. The FreeNAS installation detects all 5 disks, so I install FreeNAS onto the 128GB /dev/vtbd0, however it refuses to boot from the virtio disk after the...
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