The invention of Festool's Domino System is a major advance in woodworking. Clearly much engineering energy was devoted to the original spring-loaded register pins. When user feed-back showed those pins could get in the way of Domino use, Festool brought out a new Domino with flip-out registration paddles.
As it happens I own one of each. I was one of the first in Los Angeles to receive my older Domino, the one with the pins. In all the years I have owned it I have never located a subsequent mortise using the pins or paddles.
For my work I always draw center lines on both parts, as I do with biscuit joints. Just as when I use CADD to instruct CNC machines, I prefer absolute measurements.
There is a reason Festool provides 3 settings for mortise width. My selection is based on my expectation of the wood expanding or contracting, not to cover my mistakes locating the center line. If I am using a series of Dominoes in a line over 1800mm, I normally make the center mortise minimum width. Often I do not glue that floating Domino tendon. Then as I fan out from the center I keep the mortises minimum, gluing the others. If I expect the wood to expand or contract, the mortises on one part remain minimum and the Domino is glued into those. The corresponding mortises will be wider, with the Domino floating in them unglued.