Because the seeding was only determined by the group stages. This was more than likely to avoid the need for something to happen if Taiwan placed 1st/2nd in the knockout stage (they don't have a third seed, so what do they get).
While several people have said they should earn a third seed and then you just move it into the 2nd pool, ideally this is good, but when you take into account Taiwan's general population compared to Europe, NA, Korea, and China, it becomes pretty obvious why they have 2 seeds and not 3 (not to say that won't change, but they'll probably always have fewer than the other regions).
Anyways, back to your question, it's pretty much tradition based past the fact that knockout stage placement wasn't taken into account. It's probably a good thing too considering it's only a single elimination bracket, so technically speaking, RNG could be better at Bo5s than CLG and FW. If it were a double elimination tournament, then I could see it being used for group seeding, but I don't think using a single elimination bracket is the best way to determine the best 2 regions when it could've simply been luck.