Can you ask for a face to face to meeting the Secretariat to present your case?
Did you fill out the application form correctly as it clearly says in their policy statement you must have 5 years training?
Other avenues:
1. Go to Invest HK and tell them you want to set up a medical practice in HK and ask for their assistance. As they are quasi-gov't if I have heard their presentations correctly they can even call Immigration for example on a person's behalf just to make an inquiry. These guys are here to bring in new business and talent. Not sure if the medical side of it though but give it a shot.
2. You could go to a lawyer (depends on your $$$) and seek legal advice although based on their rules and the authority they have it might be hard to get them to be fearful and give you a second look. I'd be very cautious giving them any threatening letters if the law firm you went to really does not know administrative law in HK or had any experience.
The rule setting bodies if they follow their rules likely can't be argued with.
It strikes me from looking at the rules they are as clearly written as I have ever seen in HK and there are some very odd rules from gov't entities that defy any logic at times.
It seems that you should be able to present evidence that suggests you meet the criteria including the 12 month internship.
3. Lay out your program column by column vs HK U.
One way to do this is spend some laying out a comparison between your training and the HK Universities and do it course by course showing that you have done all that they have done including the 12 months internship.
I think the medical qualifications letter is a good first step however.
You can't be the first Canadian trained doctor coming to HK for the first time or returning home.