Suppose you let identical pith balls come in contact to make q1=q2. Would the charges be equal if the pith balls were of different size?
I'm not real sure about pith, but I can answer for metal balls...
Putting the balls in contact forces their potential to be the same. The problem is easier if the balls are separated by a distance large compared to their size. Briefly connecting them with a wire would force the potential at each ball to be the same. In this case the ratio of charges would be equal to the ratio of the radii.