@galehill The "5mm" holes, actually 4.85mm, are for Lego pegs to attach the Atomic base to Lego Technic parts like beams. Most M5stack things have Lego-compatible mounting points.
If you look under the Atom Lite, there's a small yellow M2 hole marked on the label which you can use to fix the atom to the atomic base from below. There's a M2-sized hole in the atomic base. Just screw through the atomic base from below, into the atom label and there's a thread inside.
M5stack used to supply a M2 hex-headed bolt of the correct length and a little Allen key to mount the atom on the base.
But usually just mounting the atom on the atomic base pins is enough for most uses.