If you don't get the tuner with the 3.55's, don't even think about taking it to redline since your shift points will be way off. you could possibly overspeed the engine. lets say for instance in 1st gear WOT your car normally shifts to 2nd at ~48mph on 2.73's at 6800rpms. Well on 3.55's your car tuned should shift at 37mph 6800rpm's, but without a tune it would need 8,800rpm's to shift to second at 48mph. I don't know if the rev limiter kicks in to stop you since I haven't tuned this car yet.
If you return to the factory tune AFTER installing the new gears - for warranty work - how would that work? Wouldn't you have to return the gears to stock as well?
You can still have a stock tune and leave the changes for the 3.55 gearing if you are that paranoid. In fact dealerships will install different ratio's and adjust the PCM calibration for the new rear end gearing for you without affecting the warranty.
I don't think your PCM data-logs, so I don't know why people are so worried about jumping back to the stock gearing when you take it in to the dealership. There are really only a few ways you can tell it is an aftermarket tune (higher shift points/rev limiters, WOT timing, transmission line pressures on automatics,ect) that the dealership won't be able to see unless they are driving the car and datalogging it themselves. It's not like you pull up the screen and a giant "BAMA TUNE" pops up before you can read the engine parameters.