I know you want to keep using those battered holders, but they’re fighting you every step of the way.
Eyeballometrically, each piston has about half a millimeter of clearance in its hole. You can’t expect better accuracy than a millimeter in any direction after aligning the entire pattern to a couple of pistons with inaccurate positions.
Similarly, pushing the holder around to align a spinny ring of red laser light hitting the top of a chamfered piston at an angle leaves entirely too much to the imagination.
Because Print and Cut isn’t available for Galvo lasers, you must do this on hard mode.
Machine two square fixture plates, one with zero-clearance holes to fit all those pistons, separated by four legs long enough to put the pistons exactly level with the top surface. Drop the pistons into the fixture plate holes so they’re neatly lined up. You may want a third plate with matching holes atop the base plate to ensure the pistons sit flat on the base. Make the fixture plates from aluminum and you can pick the pistons out with a magnet.
Draw a square the same size as the fixture plate on a tool layer and center it on the array of circles you made for the holder. Group all that, center it on the LightBurn workspace, then Lock them to the LightBurn workspace so they can’t scamper away.
Focus on the top of the fixture plate, frame the square, and align the whole fixture to the frame square. All the pistons now sit at known locations inside the frame corresponding to the circles in the LightBurn layout.
Clamp the fixture to the table and you’re set.
Load pistons, verify the frame position to be sure, and Fire The Laser.
I’d try marking something like aluminum foil flattened atop the fixture just to be sure. 