You really can't go by the marks unless you still have the factory original IP. My guess is that the marks are made by a guy and a chisel, and probably aren't all in the exact same spot anyways.
Basically at the factory the IP is timed, and then the mark is made. If you swap IP's from 2 motors and re-time them, the marks will probably not line up.
This is exactly right. The marks are only there for reference. Once the pump is moved or changed, the marks mean very little. When you assemble an engine, the marks on the gears internally allow you to get the pump into position enough to get the engine to run(static timing) and then once you properly time the engine with a meter, or pulse adapter, and get the timing exact(dynamic timing), essentially you could/should re mark the pump for future reference.
That's the basics. There's much more to it though. Each injector will pop open and shoot fuel at a certain pressure, so as the injectors and pump wear, then each injector is popping at a different pressure, and therefore some may be shooting fuel before others in the cycle, therefore that particular cylinder would be more advanced than another that pops later, so the timing of the pump is really only getting an average of all the cylinders. Further, since the timing is done on #1 cylinder, this means that you are setting the timing for the whole engine based on the timing for the #1 cylinder.
So, basically the line allows you to get the engine started. If your pump and injectors are fairly new, and running efficiently, then you need to get the timing set by meter or pulse method, and then this would be as close as you could get. Some say you can set the timing by ear, but it is likely not really very accurate. The amount and colour of the smoke can be a clue, but also not really accurate.
If you fool around with it, you run the risk of running advanced/retarded or hot/cold, and either situation isn't good for the engine and especially for efficiency/economy...
Just my .02
zigg