I believe that Yamaha regional distributors DO have input on the colour schemes, possibly about the only thing they control;
This year Canadian bikes are completely mono-coloured; tank skirt, side panel and grab rail the bike's color.
Euro bikes are all mono-coloured, but for the grab rail, which is silver. For years Europeans and other markets had the choice of several colours and the bikes had what some consider to be neat striping where North Americans have only had the single choice and plain paint work . . . .
US bikes have silver tank skirts and side rails and body coloured grab rails and apparently black side vents, from EricL's avatar photo . . .
Another item is the immobiliser; All bikes EXCEPT US bikes have them . . . probably because they are not required by law and to keep their costs down and because the market is large enough for them to flex their muscles in that regard. So as a result Americans get bendable keys where everyone else has good, solid ones.
Canadians don't get bag liners for some reason, where Americans (and probably other markets) do. Then again, Americans can't order the OEM footguards from Yamaha in the US and no one in North America can order the narrower 'city cases' from local distribution.
Likely everything else is regulation-driven (some markets have reduced horsepower, others (like the Canadians) can't select US/British measure for display purposes. Euro machines have no reflectors on their side cases or front forks, Europeans get 'flash to pass' and so on.
I'm certain there is likely more regional customisation. I'm glad I'm not a vehicle manufacturer.