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I beleive that the unicode consortium have chosen not to say much about witch flags are there pretty much for this reason. They don't want unicode to get mixed in with international politics.
It goes beyond that; technically, there are no flags in Unicode. Instead, there are https://en.wikipedia.org/wiki/Regional_Indicator_Symbol — an symbol-alphabet where any pair of successive symbols from the alphabet are meant to be considered a ligature (so, a space of 36^2 = 1296 possible ligatures), where a subset of these ligatures are considered valid representations of a locale from the Unicode's https://en.wiki…
Agreed. The only other way to draw locales would be to country outlines: which would most certainly open a Pandora's Box of socio political issues.
What Apple has effectively done by invalidating the locale, is to remove the Taiwanese language.
As an aside though: from a personal point of view there's quite a few emoji that I'd like to see hidden, such as the poop and middle finger. There's no need for such things, & yet this locale is removed? Weird politics.