I followed the plans with the exception of cutting off ~19" in length to get the table down to 5.5' in order to better fit my space.
Unfortunately several of the 2 1/2" pocket screws did pierce the top - nothing too terrible or noticeable, but disappointing. My wife says it just adds to the rustic feel, so that works.
One thing I did that I notice other people not doing: I ripped off ~1/4" from the edge of all boards for the table top. This gets rid of the "crumb catcher" spaces between the planks which come rounded. By ripping off the rounded edge, the boards will fit more flush and you won't have such an issue with crumbs getting in between the boards.