I have seen them all, dyno tuners setting the car up to never get 100% throttle in an attempt to smooth out gearshifts(WHY?) along with cars that would hold gears until next week before shifting. A dyno is not the place for setting up an auto to shift correctly, it takes months of data analysis on the street to improve gearshifts and even the same make/model often require tweaking of 100rpm or so between cars to optimise the shifts to suit a specific gearbox wear/age/fluid etc.
The transmission control unit is not programmable but it does not need to be, feed it the right signals from the ECU and it shifts perfectly fine