Chris, the objective is to get the cylinder the same diameter all the way down, and with its axis as straight and as vertical as possible. With a hone you have no chance of getting it straight and vertical, but you can try for constant diameter. The piston skirt travels most of the length of the bore, and it should have the prescribed clearance the whole way. That will also give the other parts of the piston the clearance they were designed to have.
