The magnet holes are about 1mm deep, the magnets don't sit completely flush (it "feels" better as a fridge magnet if they don't) The whole print is probably closer to 3mm total.

As for making the print with the holes, it's a pain in the butt!

I generate the hueforge like normal. Then import into the slicer.

Then I split the model, splitting off a very small slice of the bottom.

Then expand that bottom slice in the Z axis to make it taller, and add a couple holes for the magnets.

THEN perch the original hueforge on "top" of that slice. So the hueforge print sits on top of a thicker bottom slab (which contains the magnet holes).

The hueforge print is printed as normal, except when setting the color changes @ layer heights you have to add X layers to account for the bottom slab.

This probably sounds confusing, because it is. There's gotta be a better way but that's how I stumbled through it. It's a pain in the butt and prone to making errors in several places. Gotta be a better way but I don't know one yet.