[1] https://groups.google.com/forum/#!topic/qubes-devel/MfHy2jmX...
But PCI passthrough for gaming isn't a great fit for the Qubes security model: it requires trusting that the Windows guest cannot compromise the GPU you loan it, which makes it a much bigger risk than an ordinary AppVM.
Do you mean these controls are porous by design or are you talking about bugs in the IOMMU protections?
Next time your PC going to boot your GPU will be initialized with host BIOS / UEFI long before kernel get possibility to limit it with IOMMU.