It is all a matter of degree. Incidents can happen at any racetrack, it is inherent in the activity. But at least, the design features of the facility shouldn't present an undue risk on their own.
Calabogie was originally designed by "car guys". It was not designed to have motorcycle racing on it. At a track day, things can be done ... people can take a notch of aggressiveness off at certain areas of the track, or organizers can enforce "no passing" zones, or organizers can put down hay bales or cones to slow people down ... seen this done at a track day at Mont-Tremblant, which is not the safest track for motorcycle racing, either.
Mosport was originally designed decades ago, before any thought was put towards safety at all. Safety at that time was simple, "don't crash". Many, MANY improvements have been made since then.
Basic motorcycle track design safety: You don't put fixed obstacles in the expected trajectory of bikes and riders sliding off the track. Nor do you allow bikes and riders sliding off the track, to go over a cliff that is within their expected trajectory. Nor do you allow bikes and riders sliding off the track, to reach another portion of the track with cross traffic on it. All are potential issues with either the lower or upper level of a bridge/tunnel.
The words "expected trajectory" don't preclude one-in-a-million incidents from happening and you cannot design for those incidents. You design for the way things go down 99+% of the time. If there is a wall or a cliff face or a tree within that zone that includes the trajectory from (say) 99% of crashes, there is a problem with the design, because that obstacle is going to get hit, frequently ... The FIM rules address all of these requirements - how much run-off distance, related to what the radius of the corner is (which is related to the speed through the corner), etc.
Both Shannonville and Cayuga have concrete walls on the outside of a corner, which is not the best, but what saves those corners from being much worse than they are (I've seen bad things happen at Shannonville corner 14) is that they are both on slow corners and they are both lined with lots and lots of haybales or air fence. The "expected trajectory" is a lot shorter on a slow corner. Some years ago, the inside of the pavement was brought in at Shannonville to make the corner even tighter and encourage riders to take a path that aimed them more down the straight and less towards that wall (and this worked - riders hitting that wall happens much less than it did before). And years before that, the old (original) Nelson track used what is now an access road, as the main track. That layout had riders aimed straight towards that wall in a braking zone ... Nowadays, you just don't do that.