The fact they are carrying differnet assy part numbers would indicate something is different. The down side is that the spares lists will not go down to the individual componet depths, so if it opens all the way, you probaby have different castings, or as you say, a bigger / smaller bore, although putting my manuifacturing efficiencty hat on, I would be surprised if it were two totally differnet castings, purely dwn to economies of scale. Having said that, Yam also mke bikes,so goodness knows whether one of them is shared with a two wheeled machine or not.
Remember you also have differences in the exhast side. I still reckon if that's the case, you may be as cheap just trading in for a bigger engine.
Only way to find out for sure is go measure one.