Yes, e.g. what if you are quoting something with italics in the original text? For older texts in English, italics might easily indicate a word or phrase in a non-English language. Showing that with semantic "emphasis" might convey the wrong impression -- e.g. without a note such as "emphasis added".
The OP addresses "idiom in another language" as one case, but if it is within a scholarly quotation, can one change the typography to a different convention?
Then there's the matter of languages such as Japanese that use a different set of characters (katakana) both to indicate emphasis and to mark foreign loan-words. Would katakana characters still be enclosed in an <i> element? Would styling be modified accordingly?