And yet if I look at StatCounter's map function, showing the leading browser in each country Chrome leads in most of the world. IE only leads in Japan, South Korea, Swaziland (pop. 1.1mio), Greenland (pop. 55000) and Antarctica (5000 visitors). Firefox has a few strongholds like Germany, Indonesia, Myanmar, Bangladesh, Iran and a bunch of countries in Africa, but the only place IE is ahead of Chrome in second place is Iran (pop. 78mio). With Chrome winning on walkover in Europe, South America, North America, Africa and Oceania and taking massive wins in China, India and Russia I don't see how any possible weighting of StatCounter's numbers would put IE on top.
You're right that the country weightings don't account for the difference by themselves, but there is also the difference between counting users versus pageviews, and it would be unsurprising if there were differences between the types of websites sampled by the two companies.