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On my opinion, if you have a question on the paper that you referee, you may ask only the author. A referee is not only anonymous but also is supposed to be confidential. Which means you are not supposed to discuss anything in the paper that you referee with the third parties, anonymously or not.

I don't think there is anything inappropriate about using alternate accounts to ask questions. I have asked many questions using alternate accounts over the years (for all kinds of reasons, e.g. shame at not knowing something basic!). As long as your different accounts don't interact (and especially don't vote for each other!), this does not violate any ...