I wouldn't jump on wall clearance just yet. The engine has obviously had some material go through it, that is obvious from the piston damage and bearing condition. That quite possibly could be the culprit of the accelerated skirt wear. I have seen plenty of engines which were running the correct wall clearance end up with skirts looking just like that, only because they had material in the oil.
Generally, we run .004-.005 P/W clearance on our forged pistons, and do not see scuffing. However, different manufacturers use different alloys with different coefficients of thermal expansion. If you go too large, the pistons rock when cold [loud], the pistons overheat due to reduces wall contact, and blow-by increases. If too small, they will scuff, or at worst, seize in the bores.
I am fairly sure in this case that the counterweight DID NOT contact the piston. This has nothing to do with counterweight to boss clearance. I feel that something which was loose in the engine got caught between the counterweight and piston boss on the down-stroke, causing what you see. This is evident by the fact that none of the others have damage, and the dimples on the bottom of that piston are indicative of something very hard being tossed around the rotating assembly.