It depends how you define "accurate". I'd expect differences in mileage between actual miles flown, GC miles, and what the various different FF programs may award. MM uses the GC distance, so this may vary a little from what you get credited with in your FF program.

If you are ticketed HKG-JFK (I.e. You are just transiting at YVR) then this is how you need to enter it in MM if you want your route validated. If you are trying to determine how many miles you are credited, then it will depend how your FF program determines the distance; I'd have thought they are more likely to be GC HKG-JFK based than to factor in the stop at YVR.