This is exactly what I did. I just used a 1/4" end mill to drill proper size holes for my inserts for 1/4" bolts. I did use vCarve to generate the hole pattern. The just released replicator tool in Easel wasn’t available then. I might have decided to use it if it were available.
Photos here:
As you said, you can only mill the holes inside the cutting area of the machine, which was almost 30 holes.
As far as the grid, I found out the sharpies wear out fast on MDF. I went through 3 of them drawing the lines on my board. There is a lot more line length that what you first think… right at 300 feet worth.
–Rick