Siemens used to have a machine with board load at the front and feeders in the rear. If you apply the same offset to the feeder bank, than you would see the pick up.
Also, the very first Siemens machine had the capability to look through the hollow shaft Z-axis with a fiber optic camera. We could insert a glass with scale marks in the jaws and used this feature to teach PCB positions. In this case, you would not have to deal with any offset, regardless from which feeder bank you would pick.
However, Eclipse was looking for a method to move the board and align it, not using pegs. I'm used to an aluminum hollow shaft Z-axis and would be scared to death moving x and y while z is down.
Also, I do assume you do double sided boards as well, so, instead of mounting the PCB to a flat plate, you would rather clamp the board on the edges.
I got somehow fixed on the idea using the nozzle vacuum sensor to find the board position and correct all placement data on the fly (I would have to do that anyway if I would use a vision system).
In this case the regular nozzle would pick up an adapter slightly larger than the board holes, 4 mm diameter or so. There is a small hole of 1mm diameter in the center. Since the adapter is larger, the nozzle adapter will not insert in the board holes. Now, you move X and Y over the position of the first board hole and lower Z. You shouldn't get any change in vacuum, while air flows through the board hole. Move x step by step until the edge of the hole will block the nozzle hole. Do the other edge. Do the same in Y to get the hole center and a second board hole. I think it works. Haven't done the math yet.