I set up mine a bit different than most.
Instead of gluing/screwing a large sheet on the machine table I cut strips that fit in between t-track. The t track is screwed to the machine table. Doing it this way keeps me from having to remove over 100 screws from the t track every time I need to change the spoilboard.
This works out really well because the cheap plywood I use is 3/4 thick and the t track is 1/2 thick. I am pretty careful when I program so I rarely cut deeper than about 1/32 into the spoilboard.
I drill and c'bore the strips with a fixed pattern so that I can reuse the screw holes in the machine table. Like a bunch of other folks have said, I have the holes c'bored about halfway thru the plywood.
I don't use MDF for a couple of reasons. The dust is downright nasty. MDF does not hold screws as good as plywood. Yes, I do screw stuff to the spoilboard even though I have all sorts of t-track. Sometimes it is just the best way to do it.
BTW, the item on the table is my old vac table. It worked well but I do not need such a large one anymore.
The little wooden things that are bolted into the t track along the front edge of the vac table are what I use for stops. Just chuck up a .5 dowel, lower it to within about a 1/4 of the table, bump a stop against the dowel, lock it down and then jog over to where I want the next one and repeat. Y Zero is then set by typing in .25 on the DRO. Does not get much easier than this.
Low Profile CNC Router Vise