The models are designed with heat-set inserts in mind. The bigger holes (4.85mm) are placeholders for M3 inserts, the others (3.1mm) are for the M3 screws themselves.

Originally, I powered my Pi cluster with individual 5v power supplies over USB. This always seemed a bit hacky and I honestly just wanted to have the power delivery for my entire cluster in one place. The solution I came up with might not be any less hacky but at least everything is in one place and, thanks to the cooling fans I hot-glued on, stays cool.

Again: arguably not a less hacky solution (especially with the glued on fans), but I have been using this for some days now and I am quite happy with it.