1960-D Cent Machine Doubling?

The area you are looking at is where the devices were altered during the strike. The overall size of the devices is there, just damaged during the strike. If it were hub doubling, then you would see the devices enlarged:
Here is a DDR on the same devices:

Note the lines on the contour of the devices? That is from the miss hubbing during die creation. Note the color of the devices. Note how they go from light to darkness? On a machine damage device will have the area in question look just one color because it is flat. Also the devices on a doubled die will be enlarged.
Note the machine damage on these devices:

The devices are reduced from the damage on the devices. That is what caught your attention. You are correct about it being MD.

Means the overall size of the devices would be larger than than they typically are is all(if it were hub doubling)

On the MD the original device is reduced in size because the doubling subtracted from it. On the Doubled Die the original device is larger because the doubling is added to it.

The same event that damages the devices also alters a doubled die as well as a normal dies coins:

The movement because of hop/bounce/die movement damages the devices like a car out of control in a parking lot. It reduces the size of the devices.