Dang, I posted too quickly and forgot two important characteristics of the mysterious hole-making monsters.

5. The larger holes appear in areas with a healthy lace monitor population. I know this because I usually find them when I'm looking for lace monitors.

6. The smaller holes appear in areas where one would expect to find heath monitors.

There's a bit of overlap in hole size, of course, but I've never seen a hole the same size as the smallest hole I've found, in a lace monitor area and I've never seen a hole the same size as the largest hole I've found, in a heath monitor area.