Appropriately sized festool dominos or dowels.
1/8" and/or 1/4" bit.
Optional: festool domino machine for cutting the other piece.
Optional: dowel jig or 3/8" or 1/4" bit for drilling the other piece.
These template patterns for the festool dominos, 3/8" and 1/4" dowel holes are meant to be placed in your designs. Although not as fast as using a domino machine or a dowel jig, cutting them using shaper while you're already cutting the rest of your design should result in more accurate placement when the holes are in the middle of the board.
To use, cut the appropriate shape and paste it into your design.
Use the 1/8" bit to cut the #4, #5 and #6 domino holes. #8 and #10 holes are cut with the 1/4" bit. The wide set is just a smidge (~1mm) wider than the tight set and nowhere near the second setting on the domino machine.
I've included both the svg files and the affinity files.