I've successfully built a coreboot firmware and Linux bootloader payload for the Chell Chromebook with Skylake, which then kexec's Xen / Qubes from the eMMC. Both of them are reporting that the IOMMU is not in use, and there is no DMAR entry in the ACPI table, which I believe is what they are looking for for enabling the IOMMU.
The Xen console prints:
(XEN) I/O virtualization disabled
And qubes-hcl reports:
I/O MMU: Not active
What's involved in enabling it? How soon in the boot process can it be turned on?