If I compare two identical configurations, which only differ from each other in low wing and high wing position. We assume that the lift and drag remains constant. Will I get the same coefficients in moment for pitch, roll, and yaw? Because the force arms are the same?
For a first approximation, the coefficients will be similar enough, but not exactly identical. As you correctly point out the moment arms will be the same, but the interference effects of the wing-fuselage joint may not.
That is to say, your assumption that the lift distribution will remain unchanged will likely not hold out in reality.
The stability derivatives will not be similar, however.
If you have zero sideslip, then the moment coefficients will be similar between the two configurations. The only difference would come from difference in drag and its effect on moments, which would be small.
If you have non-zero sideslip, then the roll moment coefficients will be different due to dihedral effect.