Most machinists bore any cylinder to the diameter of the piston that's going into the hole, and put the skirt clearance in with a hone to eliminate the machining marks. The finish bore would end up 3 9/16" for a 235 Std. piston, with about .0025-.003" skirt clearance- - - -3.0625" final diameter, with the clearance built into the piston skirt. To do it accurately most good machinists insist on having the pistons on hand before they start whittling on the block, and fit each piston individually.
Jerry