Have not done anything with trying to get the bottom PCIe slot to work for host/bios. But it is intriguing. Running 4.0x8/3.0x8 has been good enough as I play most games in Linux anyway, so 4.0x8 and 5700 for host. 3.0x8 is currently running R7 370 as proof of concept. Waiting on RTX 3xxx and RX6700 for long term second card.
Also currently have this in an old Fractal R4, so there is only room for single slot coolers in the bottom slot. Hoping for a short 4u case but everything has been out of stock. Once I get a new case for this I will look into using the bottom slot for BIOS/host and top slot in x16 for VM. But given the human malware and supply chain issues that may be a while.
Side note I actually found the SVM and IOMMU settings in the overclocking settings the other day. So they are reachable without using the find function. Just not at all where I would have placed them.
Other than finding the SVM and IOMMU settings I have not had any hardware issues getting VFIO/LG working. Had one minor config issue where windows VM switched itself to 4k output which caused LG server on windows to crash instantly on launch. But after resetting to 1440 It has all been flawless. Having a PCIe 4.0 card or reducing to 1080 would reduce lag a bit but that is a problem with me waiting for next gen GPU.
As for getting things setup in Fedora I basically just followed this thread. When that was missing something or not doing what I wanted I would read up on archwiki.
I kept a text file with all of my steps end to end encase I ever need to redo or adjust anything. Because I was converting a second drive with windows already installed my steps were a bit out of order from the vfio-in-2019 thread. Have been meaning to share my modified steps. Will see if i can format and post my steps as a new thread in the next couple days.
Regarding the bottom pcie slot, I was reading the MSI Unify documentation the other day, and the page on the PCIe slots seemed to suggest that the bottom slot wasn’t compatable with graphics cards, so I would guess that this isn’t possible. I would be interested to know if it’s possible to run the host/bios card in the second slot though, as opposed to your current setup