I suppose it depends on what you intend to do with the holes. If you are just using them for the through-hole clamps, a slight misalignment will not matter at all. With dogs or the newer lever type clamps, that off-set might matter, because there would be less contact.
I have done this a couple of different ways.
The first time was done with a full-sized template, made by a CNC machine. That one was a full 1 1/8" thick, which brought its own challenges. The clamps won't fit in a top that thick. That meant cutting a huge 45 degree bevel on the underside. Having over 250 holes made that a lot of work.
The second time was with the Parf-guide system. I also had a CXS by that time, which helps a lot.
I have no idea how accurate the first top actually was, since I didn't use it with a guide rail back then. I can however tell you how good the Parf system can be. I have heard of people having issues with it, but taking proper care as you go, should yield great results. Mine is dead-on over the entire 4' x 8' surface. I did drill mine over some scrap, as a backer, but not all at one time. I did it in sections, over a few days.