If you think about the actual difference between the two, it should be obvious which one you should be using. Flat (Which is not really 100% flat-rate, it's just more flat than the other option) provides a more linear response from the spring through the range of movement in the rear suspension. That means that the resistance to the suspension being compressed more than it currently is will be more similar through the entire range of motion, so the suspension retains more ability to respond even when it's already compressed. This = Traction. With the Progressive linkage, the farther the rear suspension is compressed, the more the resistance of the spring is amplified by the linkage. That means that as the rear is compressed (in a corner, during acceleration, going over a bump, etc.) the suspension gets stiffer and stiffer the more it's compressed. This = Less Traction, since the rear can't respond as much to bumps and the tire will tend to spin/skip more as power is applied and the rear is squatting under the force of acceleration.
The intent of the Progressive setting is to resist the suspension bottoming out completely with the added weight of a passenger on the bike. For every other purpose, it's a negative effect. We've been putting flat-rate linkages on race bikes that came with Progressive linkages for a long time, this is nothing new, but what WAS new was that when the 1199 was released in 2012 it was the first standard production bike from Ducati to come with the ability to have a flat(ish) rate linkage straight from the factory. Some of the R models in the past (749R for sure, maybe others) had a flat-rate linkage on them also, but never a standard production bike. The more powerful the bikes have gotten, the more important this is since wheelspin is a limiting factor in acceleration and getting a good drive off of corners, especially on the track.
Incidentally, if anyone ever says their bike "handles" better with the Progressive setting it most likely means that their shock spring rate is too soft for them, and the progressive linkage is providing a band-aid to the situation by not allowing the rear to squat too much and running the bike wide on corner exits.
