The tune I got on my bike was done with this software (tuning link) in Advanced Mode (each cylinder tuned individually). The dyno room changed the air a minimum of 6 times a minute with huge filtered intakes and exhaust fans out the roof, along with two squirrel cage fans, one for each cylinder. The bike was allowed to cool for 30 minutes between tuning each cylinder. The target AFR was 13.4/1 at steady throttle positions, and 13/1 at WOT. Although I don't think my bike is absolutely optimally tuned (98 TQ/95 HP), and could get in the low 100's with a little more work, it's close enough for now. The tune got me about 10/10 over a "canned" map I had loaded from FuelMoto USA to ride the bike to the tuner, as it was rich.
Like any other self tuning control system, the computer is going to pick a set of acceptable parameters and tune the bike based on comparing the sniffers to those tuning parameters it is given. And expert tuner CAN do better, no doubt, but finding one is the key. I'm happy with the way my motor is running with the Tuning Link software utilized by the tuner I used, who has done hundreds of bikes. In the end, it comes down to whether it's worth 100+ more dollars in dyno time to get a couple of more numbers that may only amount to a 2 or 3 percent increase.
If you go to the Dynojet website, it lists tuners within a certain radius of you who have the Tuning Link software. It is not an inexpensive add to the normal tuning software provided with the Dyno, so even the large dealers don't always have it. My guy is a small shop, but he believes in the software for a number of reasons, so tunes with it.