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It makes up SOME with high ISO sensitivity, but only a stop or so over the best of APS (I shoot the RX1 waaaaaay beyond 3200, usually topping out at 12,800 for street work, but I shoot the Nikon A at 6400, so about a stop), and I'd say it loses a lot more than a stop of DOF, for lack of a better way to characterize it. The RX1 has to shoot at f8 to get close to the DOF I get from the Nikon A at f3.5, so that's about two and a half stops of exposure, which is more than the better sensor can compensate for.
Edit - Bart, I think this addresses your post as well...
True, but only about 1 stop of that DOF difference is down to the sensor size difference; the rest is due to the difference in equivalent focal length. If you'd compare FF and APSC at equivalent focal lengths (as I indicated in my post above), my point still holds: in terms of deep DOF, there're no disadvantages to shooting FF, but there are advantages for shallow DOF.