I played around with the ordering of the passthrough PCI devices and it now works, it required a very specific order. For my case it's: AMD Video card > SATA controller > USB controller > Sound card.
Previously I was adding the SATA controller last and it was no good.
@derickso
Everything that I used it for in 5.0 now works in 5.5U2 (which is the main reason why haven't updated until now). Passthrough configuration retains after reboot, USB works (though I'm using intel onboard controller). Also the PCI devices are better labeled rather than just Unknown Device.