Because of course when someone suggests Taiwan, what they are actually thinking of is the Indigenous people of the island (sarcasm obviously). It is very easy to find that there are more than 1 group of people that are currently being listed under the umbrella term "Taiwanese Indigenous," all of whom combine for only 2% of the island's population. Even if I try to give some intellectual credits to the original Taiwan suggestion (that somehow he meant the various groups of Indigenous instead of the ROC), how do we call that "civ"? We can't name them under an umbrella term like Civ4's Native American, and each separate group of Indigenous is too minor to justify an inclusion, and for overwhelmingly obvious reasons, it cannot be simply called "Taiwan". Even if there were a central authority for any of those groups (in this case, as you pointed out, there wasn't), any "Taiwan" suggestion, ranging from the ROC to the various Indigenous groups, is a poor suggestion.
And just for the record, Taiwan is the Chinese name for the island, so it is only normal that every mention of that name will bring with it an implication of Chinese influence. Since most of these Indigenous groups don't speak a Sinitic language, I'd assume they call the island differently.
As for Tibet, it is inarguable that they have everything required to be presented with a good Civ design, but we won't get them because of obvious political reasons. We have more chance to get Israel than Tibet, so a close representation of Tibet like Bhutan or Nepal is the best we can potentially see.