I conducted a little bit more google searching.
Some engine builders report different offsets in Left bank and Right bank pistons that have come out of Porsches and VWs. And those engine builders do not know why and don't know how find someone that would know why. There might be some more manufacturers out there that do this, but most people don't measure the piston bore offset when disassembling a motor. These builders have built them all different ways. Some with zero offset, some like they were disassembled with zero offset on one bank and 0.020" on the other bank, some with 0.020" offset both banks with little discernible difference. Some have even installed the pistons with 0.020" in the opposite direction for a couple more horsepower with a trade off that their motors sounded like "cement mixers".
As pjtoledo stated, some manufacturers offset the cylinder bore in relation to the crank centerline to gain offset, however this is mostly done to save in parts cost by being able to cast and stock one piston instead of two. So, in our V6 motors, that advantage would be mute unless there is some other reason Yamaha offset bored the left bank of cylinders and offset the piston pin in the right bank. I wonder if Wiseco, when they make those pistons for SHO NUT, use the OEM offset or 0.020" for both banks? I will email Josh and see if he knows.