Auto boxes these days are wear items, especially if it's connected to a big engine driven a bit faster than average. It's not hard to see that a powerful engine with a more aggressive tune than factory could easily have a negative impact on the auto box. I suppose if auto boxes cost not much more than brake pads then it wouldn't really matter but if you are counting pennies I'd definitely take heed of the potential for the box needing attention in the not so distant future.
