It would seem the smallest possible flap deflection to produce the desired lift would be the best solution. What I experienced on the Sagitta was a flap deflection of only about 15 to 16 degrees necessary for about 30 degrees of elevator deflection to produce an excellent hard corner with a flat recovery.
This means that the interruption in the wing surface would actually be relatively small, and easy to slightly inset into the trailing edge.
Certainly there are many other factors in this situation...for instance Al's experimentation was aimed at producing maximum lift with his airfoils, not producing the most efficient lift in terms of lift vs drag.
Higher aspect ratios with lighter wing loadings do not need to sacrafice with higher drag ratios to achieve the DESIRED lift.
Al's Semi-Scale airplanes had relatively high wing loadings and needed large flap deflections to produce maximum lift for a given speed. My 50 oz 650 sq in Sagitta did not.
My point here (if there is one

) is that the flap design is not an independent factor but should probably be well considered in the overall requirements of the airplane design.
Based on personal experience with "wimpy" flaps I think flap and wing stiffness is one of the most important considerations in making an airplane that is predictable to trim, especially if a hard corner is desirable...
Randy Cuberly