That is correct. The person who originally made the patch was using Arch, but he had a virtual machine running on Arch and ran into the same issues as we are running into now. Making these changes and a few in syslinux solved the reboot VM crash for him.
He modified his sysconfig to look similar to the one I have set up here:
label unRAID OS (Elgato Fix)
kernel /bzimage-new
append pcie_acs_override=downstream pci-stub.ids=<removed>,12ab:0380 vfio-pci.ids=12ab:0380 disable_idle_d3=1 initrd=/bzroot-new
EDIT: Making progress! I just took a moment to step back and think about the steps and realized that this whole time I've been trying to compile both bzroot and bzimage, but I haven't really been doing anything to bzroot, but extracting and recompiling it (wrong, I might add). I was replacing bzroot for no reason, so I used the bzroot that came with unRAID and the bzimage that I have been compiling, low and behold, I CAN REBOOT! There are some issues with the card still, but I think they may not be related. It's just weird, it prompts me to reboot to finish installing the drivers, but when I reboot, that message doesn't go away and the card still doesn't work. I'm wondering if maybe Windows isn't shutting down cleanly...