Ah yes, the eternal question......
As far as i can tell, EVERYONE is right to a degree! Whenver a new model is tooled up there are so many factors involved in its final demensions - crossover of existing parts from other models is definitely one of them. Minimizing costs/maximizing profits is the primary goal of a corporation after all.
As well, to stay within key design parameters, and in order to keep machines within a desired displacement (be it for racing or just keeping up with the competiton), certain compromises will always have to be made. Changing the bore or stroke up or down 2 mm may seem like a simple thing to us home tuners looking to draw an extra few horses, but to the engineer at the drawing board starting from scratch it really must be a huge nightmare - sorting out piston speeds, reciprocating mass variables, surface area heat transfer, cumbustion chamber turbulence...........
Well we all get the idea........ sooooooo much easier when theres a set of slugs or con-rods sitting there that he knows about every single variable already!!!!
Here's a fun idea though - who's machine (any make) has taken the greatest license with rounding their displacment numbers

??
I had an '83 yamaha XJ 900 that was 853cc - shoulda been an XJ 850 maybe??