Just the opposite. For the transmission, a
Black Bear tune tightens up the shift points so that it doesn't slip the clutches in the transmission like the factory tune does, thus extending their life. For the engine, they turn off the AFM system which avoids the costly problems that can come with that over time. And, they will tweak the fuel and ignition tables to optimize fuel and spark delivery to increase horsepower and torque.
The only downside is that you need to run premium fuel with it, although they can also tune it so it will still run 87 if you prefer, but you won't get as significant of power gains. As James says, they do this by selling you a datalogger/programmer that will read the current engine and transmission parameters while you drive a prescribed 20 minute cycle. Then you email the files it generates to Black Bear and they email you back a tune file a week or 2 later that you then apply with the device. Super simple. I also used them to set up my tune for a new cam, and they did a beautiful job.
I prefer their approach to a 'canned' tune, because it's a tune made specific to your vehicle and preferences, and not just generalized settings tweaks.