Every orbit contributes orbit size times stabilizer size, or |G|. Therefore the total is |G| times the number of orbits. The sum of χ(a) produces the same total.
Another form of the Burnside counting theorem lets G act on S cross S by permuting the individual components as before. The number of elements fixed by a is now χ(a)2. The sum of χ(a)2 is equal to the number of orbits times |G|, as before.
When the action is doubly transitive, every pair is mapped to every other pair, so only two orbits are present, x,x and x,y. Thus the sum of χ(a)2 = 2×|G|.