If you flat shift at 5,500 rpm on the stock ECU you have plenty of head room and do no harm. I do it all the time, have put 33,000 miles on the car now and have had no problems on stock tune. So if the AP softens the shift a bit, then that's even better.
When Car and Driver first tested an early '07 MS3, a Mazda engineer even encouraged their test team to flat shift this car, saying "go ahead, it won't hurt it." They did and it did not hurt it.
Well, if you are really stupid and don't know how to flat shift, or if you try to be even more stupid and try to shift above 6,000 rpm, you might hit the rev limiter. Even then, that's what it is for to prevent over rev via accelerator or throttle plate position. But bouncing off the rev limiter too frequently could have some possible negative effects.
Done properly a flat shift does not harm the engine or the drive train. If it had, I would have experienced it a long time ago and I'm probably hundreds of flat shifts into it now.
Just one opinion. If AP can soften it a bit, I see no reason not to do what I and others are already doing sensibly with upshifts where they ought to be anyway, 5,500 to no more than 5,800 rpm.
