I designed and built a canard with flaperons and leading edge slats a few years back. I found that I could not use the slats, let alone the slats without the pitching moment of the airplane going way beyond what the canard elevator (full flying in my case) could handle. So you are absolutely correct that a flap arrangement had better take into account the pitching action. And, it is not the change in pitching moment of the airfoil section itself but the fact that a canard is a BIPLANE and the rear plane, in my case, suddenly had tons more lift than before.
The Beech Starship, as I recall, has flaps but the sweep angle of the canard surfaces changes to move the canard forward when flaps are deployed, which is clever. I assume it works.
The big problem with your idea is that you are adding a third major surface which will affect the np of the airplane by moving it way forward, just as if you moved the main wing or added surface to the front of it. I suppose you could add a surface that "weathervanes" in such a way that no lift is imparted to the fuselage until you power it into an angle of attack??
Good luck.
Allan
Here's a shot of my canard (currently a hanger queen because it was just too heavy and complicated)