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.

Thanks to both of you for the great tips and helpful explanations. Good to know also about the differences in strength resulting from different placements of the domino in the edge of the board, and about the 4mm ones being more useful for alignment than strength. That's OK in this case, I just want them for alignment. This box is rather small and I want to maximize the available space, that's why I'm using 1/2" plywood instead of something thicker. It doesn't need to support a lot of load.

I went with the 10mm offset line, I first drew a center line where I wanted the dominos to be in the face, and then I drew another line 10 mm below that and clamped a board to that line. I then referenced the machine's bottom plate from the board (and the horizontal position with the cursor and another pencil line), and it worked out great, the placement was spot on.

I also read that the part of the machine highlighted in the one photo below is indicating the center of the cutter (i.e. it's also 10mm from the bottom), that's helpful as well to double check.

Between recently finally figuring out how to precisely square my MFT/TS55 and get accurate cuts and now adding the Domino, this project was very satisfying, the last one was frustrating in comparison.