My 550 is the same set up...
I've been fortunate I suppose but I haven't seen the so called flat spot.
The comment you made about it being RPM based and not really throttle position.. makes me think of the power band of the bike.
I rode my 750 for a few years before getting the 550. The 750 still pulls like a truck even at lower RPMs... the 550, as mentioned above, really comes alive over 4k RPM.. I find myself downshifting a lot more in rush hour traffic.