The clinical judgment is a matter for the treating doctor, but he has to operate within the limits of the provincial insurance policy. The insurance policy generally does not cover routine circumcision, but does cover circumcision as a medical necessity, The doctor is free to provide the treatment in any case, but if he wants to claim the cost from the provincial insurer (as opposed to from a private insurer, or from the patient) he has to make (and stand over) the clinical judgment that it’s medically necessary, and he can’t rely on a judgment that it’s routinely medically necessary, since routine circumcision is explicitly not covered; he’s going to have to point to a particular medical necessity in this case.
As to what’s the process if the insurer wants to challenge the treating doctor’s clinical judgment as to medical necessity, or have it reviewed by others, I don’t know. Presumably there is such a process, but I get the impression that Canadian doctors spend a lot less time justifying or defending their clinical judgments to bean-counters than their US counterparts do.