The head diameter is not relevant for the calculation. I already posted about not staying in one spot for an extended period of time. The 5 second dose per 1 cm^2 is no more than the inverse of the movement rate - 1/5 cm^2 per second. See the derminator 2 manual regarding the calculation if you are still confused. Again, the amount of time is the average amount of time spent in a unit area; that is, I have simply given the rate at which one should needle if using D2. The D2 is also meant to be used in a constant circular motion. Used correctly, you will not hit 533 wounds three times. There should be no pausing. Hence the last bit about imagining each area receiving a total "dose" of about 5 seconds of exposure. This does not mean stay in one spot for 5 seconds. It also does not mean doing 1 cm^2 at a time, as that is too small of an area compared to how widely spaced the needles are, which I believe is what you take issue with. Rather the right technique is to evenly and in circular motions cover a large area, all over, over and over, until a total amount of time of [(area covered in cm^2)*5 seconds per cm^2] is reached, yielding an average time of around 5 seconds per unit area, or moving at an average speed of 1/5 cm^2/second. The average values are not the instantaneous values during treatment but with homogeneous passes, you will achieve something close to average.
Arguably, many passes in small circular motions at a lower frequency will give a more uniform hole distribution than a 12 needle head oscillating at 120 Hz aiming to get all the holes in a single pass - the latter is much more prone to the same-hole-striking problem you are concerned about, unless the motion of the needle and area covered are controlled very well. This is likely why Follica has arranged its needle head in a linear array and recommends a "lawnmower" pattern of treatment in its patent. On the other hand, the Derminator 2's manual explicitly warns against moving in a linear motion and instead suggest constant circular motions as the needles themselves are arranged in a circular pattern. The Derminator 2 cannot be used to make linear passes with a constant velocity, or else you are correct that it is possible to overlap holes if you move at a constant velocity that is the average velocity and want it done in one pass. The D2 is not designed to achieve a hole density of 1600 holes/cm^2 in a single pass lawn mower pattern. Hence we calculate the time to spend per unit area and make circular motions over a large area until we average 5 seconds spent per cm^2. The hole distribution will be quite random if you keep the head moving in small circular motions constantly.