If you have a dremel and a 3d printer (which it sounds like you do but I can't quite figure out if you're talking from experience or research) you should print this -
Drill press for a Dremel
You could also make a jig out of wood/plastic/etc. for a regular handheld battery powered drill if needed. All you need is a little ingenuity and you should be able to easily countersink those holes in 15 minutes or less after obtaining the proper bit and creating a jig that has the travel you want for the depth of the countersink. ;)
Very cool, thanks for sharing!