Certainly justifiable and not an arbitrary measure since those MCT times are actually well thought out and normally based on empirical data gathered on the time it takes passengers to get to various gates around an airport. But I think too part of it would depend on the context. For instance, I once had a tight connection well below the MCT for ORD and was certain I'd miss the connection. However, to my delight, my UA plane from YYZ arrived 2 gates away from the connecting HNL flight. So in some cases the airlines can coordinate to minimize the risk of misconnection (e.g., United's
ConnectionSaver technology).
I suppose part of it depends on things like whether they could safely hold the plane for you. Having flown long haul quite a bit, a 30 minute or even hour delay won't necessarily impact flights since they can often make up the time in the air, particularly on longer routes like SFO > SYD.
Well I'm not sure whether you could claim MC99 for something like that since the injury was caused by the passenger's negligence. Certainly if you misconnect and your trip began in Canada or Europe, compensation could very well be due, as it is based on when you arrive at your final destination, and so even if your flight into the connecting hub was 45 minutes late, and that caused you to misconnect into Sydney, where you had to wait 14 hours for the next flight, then considerable compensation could be owed (to say nothing of meals, hotels and damages pursuant to MC99).
-RooFlyer88