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The main problem is just getting TrueNAS access to the physical disks via IOMMU groups and passthrough. HBA cards are a super easy way to get a dedicated IOMMU group that has all your drives attached, so it's common for people to use them in these sorts of setups. If you can pull your normal SATA controller down into the TrueNAS VM without messing anything else up on the host layer, it will work the same way as an HBA card for all TrueNAS cares.
(TMK, SATA controller hubs are usually an all-at-once passthrough, so if you have your host system running off some part of this controller it probably won't work to unhook it from the host and give it to the guest.)
Makes sense, thanks for the info
That was one of the things I got wrong at first as well. But it totally makes it much easier in the long run.