I highly recommend Profili, it is a great program for the small cost.

I agree (not that it is in any way necessary :-) that for flying wings a section Cm is a really big thing. For airplanes with tails it is a small factor by comparison to what the tail or elevator inputs and so can be ignored in the analysis for the most part.

The reason that the CGs can be ran so far aft on a lot of planes is that the Neutral Point is also way aft because of the tail volume thing. I have seen free flights with the CG aft of the trailing edge of the wing. The longer the moment arm and bigger the tail the futher aft the Neutral point is. The Neutral Point doesn't change with varying camber but the tail deflection or incidence angle of the stabilizer to trim the airplane will change with camber.

Take for example a glider that is flying with a given setup. It has a certain stability determined by the CG location. Assume it has a tall T tail to get rid of downwash effects. Lowering flaps will cause an increase in lift and a negative moment (nosedown). The stability of the airplane has not changed but the tail will have to be changed to a more negaive setting to balance the moments.