Well as you know anytime you mod your car your warranty will be in question and you are running a risk (always mod at your own risk) however with the eflash set up you can flash it back to stock and "should" be ok. I can't guarantee you will be safe but from what I have read on the forums there are some dealers out there that won't give you to much hassle on certain mods.
As far as the difference being noticeable yes, VERY noticeable. the car really pulled and was a lot more throttle responsive. I have had 3 other e92M3 so I had a little bit of a history to compare the differences and I would highly recommend going to the tune.