Well, it doesn't change the gearing, as in the ratios, so it's just the degree of control that changes. I don't see how that could be anything but good.
I've always felt that the "D" change points are too low and the "S" change points far too high. Kick down can just make you look a prat, if you flick down a gear, manually, and boot it. Lost in space with loads of noise and only a liitle increase of speed. 😡
Edit:
....but, reading it all again, I see what you mean about it being set up to suit the engine tune. I find some of the gearbox changes are a bit difficult to understand, too. Guess the only way would be to try a car with the gearbox re-map.