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Perhaps you can use GPS and Wi-Fi in those certain countries but the 6D bumped up against regulations that only allow an approved class of devices, e.g., smartphone and not cameras. In the USA the Feds pulled the frequencies wireless mics operated on a few years back so manufacturers were forced to switch to other frequencies. Those types of things don't a totalitarian country make, but merely different laws for that country.
That makes good sense. I was also wondering whether Japan and other countries might have export restrictions with certain trade partners which necessitated the manufacture of a "plain" 6D. Whatever the reason, bottom line is that the 6D exists in two different configurations.