Quibbling a bit with the details here.
> This is not at all specific to ESXi... you can do PCIe and USB passthrough with qemu running on Linux.
This is true.
> The operating system doesn't get in the way.
This isn't, really, at least not qemu does quite a bit of fiddling under the hoot -- without VFIO or legacy KVM pass-through, the operating system very much gets in the way. Linux now provides facilities that allow qemu to pass through devices -- that is, it provides the APIs necessary to move it back out of the way.
I don't know to what extent ESXi looks like pure-kernel setup of passthrough vruss KVM_ASSIGN_DEVICE versus VFIO -- that would be quite interesting.