I am working with IPA annotated contents and I have linguists in my team. I understand your point (or at least I think I do), but I don't entirely concur. IPA tries to very accurate and thus covers all languages (even the click consonants used by some endangered African tribes). When you have this kind of precision employed in the context of a given natural language, you get the problem of having multiple phonetic transcriptions for the same word or syllable, all valid because from the prospective of a speaker of that language all sound the same. Yet, only one option is the closest to the pronunciation formally supported by a given authority. All you can do is to pick that one when you have to provide, and to just tolerate all the rest when you have to accept. I can hardly imagine something better than what IPA is already offering without loosing the neutral nature, so I'm yet to find valid critiques at IPA's address.