These updates fix a variety of problems that may have been overlooked when the original software was written. Vehicles will often develop issues after months or even years of driving that are corrected with a software update. It is always a good idea to have your vehicle checked for software updates, incomplete recalls, and Technical Service Bulletins.
Some transmission shops may not have the ability or equipment required to do programming and/or reprogramming. There are many shops that do though, and they should be considerably less expensive than the dealer.