Yeah the longer rod is going to put the piston further out of the hole. You could have a shorter stroke but then your port timings will be off. Spacing or cutting down the cylinder is the only way to fix that.
I think some of the clones like wallaroo have different spacing, maybe that's the rod issue? Maybe the crank is meant for a different clone bike or something. Lots of weird nos parts from different markets floating around with treats and dos scouring the globe. Also they made different weird racey shit over the years that turns up every now and then.