Those instructions have me referencing the cut from the bottom of the tool, which is 10mm from the cutter center. That seems too high and way off center for 1/2" plywood. I can see how only that bottom surface can be conveniently used to reference both when cutting into a board's edge as well as when standing vertically to cut into the side board's face, and I can see how that works great when the board is a bit thicker, but what do people do in this situation with thinner boards?
With boards thinner than 20mm the technique you posted will displace the domino toward the
bottom of the horizontal board, leading to more material being
above (and resting on) the domino - which is actually good for stability as height carries load. For a shelve the amount of material
above the domino determines the maximum load the horizontal board can take before the domino breaks through the top surface. Bringing this to the extreme (with a horizontal board too thin for the mortice being fully located inside the material) basically turns to domino in the vertical board into a shelve pin (sitting in a matching groove in the shelve) for the horizontal one .
In case you don't want that asymetry but the domino located at the center of the hozizontal board you'll have to attach a shim (thickness 1/2 of what's missing to 20mm in your horizontal boards thickness) to the upper face (that will fold down to the vertical board) of horizontal board prior to marking the reference line (the one you fold down on) which you'll then mark along the shim (not the board). Centering the domino that way in a thinner horizontal board might lead to a shelve with lower load capacity.
A 4mm domino IMHO also dosn't add relevant amounts of structural strength (compared to total glue surface), I use these more as alignment helpers for glue-ups or (what they're AFAIK intended for) stuff like picture frame corners.
Depending on how 'small' your box is you might want to use thicker material (and dominos), as plywood tends to sag when used horizontal without support.