[Ænema]

I have a manual transmission and have only spent a couple days driving a 6AT so I can't give you any real great tips, however i've read from a few guys that if you're VERY careful with it in M mode you can feel it hit a stop before it hits the kick down button.

Before making any attempt to fix any boost over shoots you need to be sure that's what's going on. If the throttle closes because of traction control then it will cause a boost spike(the TMAP sensor is pre-throttle body, so that means that throttle plate closures will spike boost pressure in the charge pipe.) Get some good DSC off 3rd gear logs.

IF YOU'RE HAVING BOOST OVERSHOOT CLOSURES:
In order to fix the boost over shoot you'll need to use the ATR software.
There are a couple ways to do it(in MOST cases, some cases may require special attention but yours should be taken care of.)

1)This is the more involved, but most accurate way.
Log Boost setpoint factor and MAF req WGDC and then back off the values(a good rule of thumb is reduce the current value by 10%) in the WGDC base table around where the boost overshoots occur.

2)This is the quicker, dirtier way of doing it. It shouldn't cause any problems but it's just not the preferred way IMO.
Simply open the WGDC base table and reduce ALL cells by 10%. So 57% becomes 51.3%, 6% becomes 5.4% etc...
It still takes a couple minutes but is a little less involved.

Once you make an adjustment then save the map and flash it to the car and log and see how it looks. If it's good then you're done, if not repeat.