It's good that you're being cautious here.
If I had to guess what section of the engine that Ducati spends the most time and money on - engineering, dyno development and racetrack testing combined - I'd pick the cylinder head. This is where combustion chamber shape, valve technology, ignition, and air flow optimization takes place and it is the key component to more engine power.
Unlike earlier engines, current head designs are the culmination of previously unavailable computer-based analytical techniques and sophisticated test equipment combined with current race track experience. In days past, engine design and manufacturing techniques were quite crude so when performance increases were in order, porting and polishing were an effective hot-rodding technique to create smoother and more complex intake and exhaust tract shapes than mass production casting techniques allowed.
With today's casting technology, there's very little to be done, or gained, in smoothing the intake and exhaust tracts since the real constraint on air flow into and out of the engine is the valve number, diameter, lift, and opening duration. A mirror-smooth port can even reduce efficient mixing of the incoming fuel and air.
Using a flow bench to improve flow rate by making gross or subtle changes to the contour of the inlet and outlet tracts is an entirely different matter. In this instance you're betting (your cylinder heads) that the machinist knows more about compressible gas flow and vortex-induced fuel-air mixing theory and practice than Ducati experts. You're also betting that he gets an improvement without benefit of any dyno development work.
There are still some practitioners of this labor intensive (i.e. expensive) craft however, and armed with a flow bench that clearly shows an improvement in air flow through a cylinder head (without valves, I might add) there are still plenty of customers who buy the story that increased air flow to and from the valves will give them more power.
Frankly, I wouldn't let anyone take a grinder to my engine before seeing a before-and-after dyno chart of - just the gas flow modification - on an identical bike.