VT-d support needs to be specifically enabled by coreboot. VT-x can be enabled in software with a 'wrmsr' command, but VT-d requires iommu to be enabled from coreboot and DMAR ACPI tables to be created.
More information here : https://forums.puri.sm/t/clarification-on-librem-15-and-intel-me/1242/11?u=kakaroto

More specifically, here are resources linked in that forum thread that are related to this :
http://coreboot.coreboot.narkive.com/9qBoAnpM/vt-d-support
https://firmware.intel.com/sites/default/files/resources/A_Tour_Beyond_BIOS_Using_Intel_VT-d_for_DMA_Protection.pdf
https://mail.coreboot.org/pipermail/coreboot/2015-August/080245.html
https://www.mail-archive.com/coreboot@coreboot.org/msg49420.html
https://groups.google.com/forum/#!topic/qubes-users/bHQHjXqinaU

Note that gm45, and ivybridge has support for VT-d, it just needs to be ported to skylake.