In my opinion, the "that" in question is grammatically correct. We're allowed to add commas for clarity. I don't believe the comma rule you quote applies here.
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jasonleeSo, I think the 'that' could be right or wrong, according to the writer's intention.Yes, but where does that leave you? You have only the author's words to guide you to his intention. Obviously, you choose the interpretation that makes the author right. So the antecedent of 'that' is most probably 'factories'.
AvangiThe ultimate life force lies in the mitochondria, that burn nearly all the oxygen we breathe in.Incorrect. Contradictory. Purely from the surface appearance of the sentence, the comma says the that-clause is non-essential. that itself says it's essential.
jasonlee1) The ultimate life force lies in tiny cellular factories of energy, which is called mitochondria which burn nearly all the oxygen we breathe in. -> grammatically right?No.
jasonleebecause the ‘that’ is wrong when the antecedent is ‘mitochondria’.I'm afraid I don't follow your reasoning on this one. I think it's just the comma that's bothering you, but it shouldn't, because it's just closing off the phrase that started with the previous comma.