I think the pencil grid is just for reference to the flatness of the hone you'e lapping. If the pencil wears away only on the edges with a few laps, then you know the stone was way off from being flat. I heard someone (probably Josh) also say that once they have lapped completely flat the first time, they re-do the grid and give a couple laps. That's all it should take to erase the pencil and you will know it is flat.

Also, I know nothing about micrometers, but isn't it possible that with ANY machined product, even digital, there could be a variance in its measurement? i.e. 0 to a micrometer that may be off could really be 0.0001 or something so that over a large measure, the number will be slightly off, if only by maybe .001"?