could a function be added to the firmware to allow individual movement of each tower?
Then we could fasten a dial indicator to the carriage and command it to move say 25mm then measure the actual movement to determine your actual steps per mm.
Likewise, measuring each tower individually could help getting belt tensions all the same. That is if the belt tension really does change steps per mm, which personally i think it can.
You don't need a special function -- just jog down 25mm using your favourite computer interface. All three carriages move, but that doesn't matter for the purposes of this test. There's no delta calculations when moving straight down.