Ostensibly, RT just objectively aggregates critics’ scores. So if you disagree with a rating, your issue is really with the critics, not with the system that merely collects the raw data.
But with borderline cases (mixed reviews), it appears that RT becomes more actively - and therefore more subjectively - involved. To wit: they’ll either 1) interpret the review as either fresh or rotten (so as to conform to their own, internal binary scheme); or 2) reach out to the critic to clarify how the review should be tabulated (again, using the binary scheme). Thus, sometimes 3/5 or C+ are recorded as fresh, sometimes the same scores are rotten.
In my view, RT should avoid “interpretation” as much as possible. So a 3/5 should always be recorded as fresh - because 3/5 is 60% and 60% is fresh according to RT’s own criterion. And if a critic objects, the onus is on them to score the movie with a rating that’s unambiguously below 60%.