I see what you are saying about fueling being affected, but I have a hard time believing that the flapper has no effect on exhaust back-pressure. At lower revs, the flap is closed...doing almost exactly the same thing that a jake brake does on a diesel. I also get that at idle it is meant to be open, but there is certainly some crossover in the transition between throttle positions.
Sure - but back pressure is different than engine braking.
I'm not an engineer I just play one on the internet, but I've had mufflers fall off cars and power dropped a lot.
I think what happens is that there is overlap between when the exhaust valve closes and the intake opens. At this point the decreased back pressure results in both the exhaust and initial gas charge being sucked out. The remaining charge is less - lower power, perceived smoother operation.
Machines with decreased back pressure have to be tuned to compensate for it. Just removing the flapper won't do this. Also, from what I've read, the flapper isn't just open and closed, it varies with operating conditions.
I guess I'm just saying the OP should ride and get used to the bike, and after a year or so, if he wants do modify stuff, have at it. I found that after a year, I was just riding the bike and using what it offers. A sharp throttle and engine braking - I'm set up for a curve without touching the brakes - in town I short shift to 3rd and things smooth out, bang down the gears - a touch of rear brake - and I'm ready for the next run - etc.. Don't baby it.
Ducati isn't the answer to everything, but they've engineered the dynamics of the bike pretty carefully- sharp and precise. I'd be leery of trying to turn it into something it's not, before understanding what it is. I was very happy with my Honda, and the duc was a shock - I adapted, it broke in, and excepting some mutually cantankerous moments, it's a pleasure to ride.