There is not actually any good reason that I'm aware of for 'reputation' to be calculated at protocol level. If a condenser created a better reputation methodology that was found by users to be more meaningful, it would become a feature that attracts people to that condenser.
Better reputation calculations are not something any condenser marketing as their 'competitive advantage', as far as I know.
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Right now it is a chain level calculation (to the best of my knowledge) based strictly on votes. IMHO a very abusable system. I only see a free downvote pool as making it more abusable.
100% accurate.