As long as I’ve been doing engines, manufacturers always use a known always constant measuring point. That in this case being the gasket surface to the outside fan hub mount.
I haven't taken one of these pumps apart...beyond taking it off the car. But is the hub a constant point? It looks like there is a shaft, with the hub on one end, and the impeller on the other end. I imagine there are a couple bearings in between. It looks (and I could be wrong) that the hub is press fit on the shaft. If that were the case, I think that maybe the hub wouldn't be a constant point. I would think the best, constant points would be the gasket surface to the end of the snout (option C). I agree that "opton D", which takes the entire bolt holes on the engine into account would be a goofy option...but it's the only one that matches on the pump in my hand. It's a reman pump...maybe it came off a different car.
At this point I just want to get it back on the car. The pump didn't come with a divider plate and mine is a little rotted. so I have to wait for a new divider plate. I was hoping today, but no order acknowledgement from Ames yet.