In fact, the CMA has done it's own earnings analysis, because the government stops at the job classification and doesn't dig to actual equal positions or specialties.  Women trend towards Psychiatry, Family Medicine, General Practice, and men trend towards more lucrative specialties, so even among "physicians", there's plenty of room to see wage variance because of personal choices around specialization and practice. 

In addition, men see more patients and bill more to the province.  That's not necessarily a benefit, from a care perspective, but it definitely ups their earnings relative to their less busy female peers.