You say that, but when I tried the GX2 crankshaft in the GX5-R, I found that the rod would rub on the crankcase, as there was no longer enough tolerance machined into the groove for the rod to pass cleanly.

Furthermore, simply measuring one of those gold tini coated GX5-R crankshafts vs a GXII crankshaft you can measure a difference on the crank pin, 0.02mm.
(Yes, brand new crankshafts)

I think the reason the rod rubs on the crankcase is that since the pin is thicker, this puts the rod further out towards the crankcase.

So I don't think you can say they are interchangeable.