I have two KVM servers where I'm doing GPU passthrough to a VM. Both are 
running linux 4.6.4.
We're using an NVIDIA GPU which means I have to hide KVM (kvm=off, or 
<kvm><hidden state='on'/></kvm>).
As a result, current_clocksource is tsc. ntpd shows a drift of ~0.
So in seems that the tsc values the VM is getting are adjusted.
On the same server, non-GPU VMs do get an unadjusted kvm-clock.

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