I cannot speak to the MK2 version, because I have the original, but as I understand it, the whole point of the MK2 was that you don't drill "directly" through the rule. I assume that the thought was that over time (and maybe some poor handling) the holes would be worn by the drill bit, causing accuracy issues.
With the MK2, the holes in the rules are larger, to accept the guide bushing, thus insulating the rule from the cutting forces of an errant drill. However, this also introduces another clearance/tolerance point.
All in all, if you follow the directions, checking those opposite points before drilling, an adjustment cn be made.
I find this system, (V1) to be very accurate. My assembly table is 49" x 130" with the grid covering 97" of that length. This goes well beyond what the sticks (rules) can do in one length, yet it is dead-on everywhere. I have tested it, years after the original drilling, with a TSO MTR-X. This triangle can "prove" the squareness of the grid at any point, because the dogs will not fit if there is any discrepancy.
I didn't have the MTR-X at the time of drilling, since it is a relatively new item, but it sure shows the accuracy of both. The MTR-X can absolutely be trusted, because it can be turned over and used on the opposite side. If anything was off and you just randomly "found" a place where it fit, turning it over would expose the flaw immediately.
It's not because of sloppy holes either. If there is anything that people have issues with, it's that the holes are too tight sometimes. Whether it is cheap, fuzzy, MDF or humidity swelling it later, who knows? but loose holes are not the reason for the fit, in my case.
I am just one guy, anecdotal evidence at best, plus I am not even using the exact same system, but it can and does work for a lot of people.
Here is the square, with 4 dogs in different rows/columns. There would be no reason to use it this way, it is totally locked up, in this position. It was just a test, when I first got it. There is some parallax error to the photo, but it is dead-on. I slid other dogs into the open holes while it was like this.
IIRC, mine is 25 columns and 13 rows, 325 holes.