You're right, each motor left the factory with a custom scribe mark. The factory would set the timing, and then make the mark for future reference. The rebuilt pump will have the scribe mark left from the original setting, not the rebuilder. So, when you install the new pump and line up the marks, the timing will be close, but probably not perfect. The best thing to do is line up the marks, start the engine, and if necessary, adjust the timing to get the right amount of diesel "rattle." Of course, adjust the timing with the engine off. Once you get the timing set where you think is about right, it would be a good idea to get it checked by someone who has a diesel timing light.
I ran mine for years having just set the timing by the hearing method. I had it checked after that, and it was nearly spot on where I wanted it performance wise, which was advanced more than the factory specs.
Casey