I can see both points of view, honestly.
I think the difference between 100% original assembled in the factory and 100% original parts comes into play when the object (guitar, bass, motorcycle, etc) is more of a hand-made item.
For instance, lots of guys need original fenders for their Indian Chiefs because the originals are missing. That's fine, they are out there. The problem is that they will get ORIGINAL fenders, prep and paint them and then they won't fit on the ORIGINAL motorcycle. That's because the fenders were handfitted at the Indian factory and the holes hand drilled in the fenders to match the fittings on the frame, which may be in slightly different locations on each bike.
On an assembly line motorcycle (or anything else) the parts are totally interchangeable and it seems less important whether it was built at the factory or at a factory dealer.