I'll disagree on the rod length being the best way to get the edge of piston flush with the top of jug. If your lowering at the base you would shorten port durations. If you deck the top there is no chance in ports.
There are a lot of variables on these engines so there is no standard. I have found decking 1mm on most will get you very close, and any more risks bouncing the piston when using a stock slant plug head, again no standard I have had them bounce at 1mm removed. Some of the stock heads enter the chamber as much as 2.5mm before curving up so the gasket thickness is not enough for clearance unless you mod. the head or go after market.
I'm guessing the head on your 50 dosen't enter the chamber before rising. The OP says the new and original pistons are the same, so even if they shipped him the 69.5 mm jug it shouldn't stick up as much as he is saying if at all. Maybe he will post some pics. and clear up this mystery. The only way I see it poss. is a type piston in b type engine.