I agree trying to short-check a bag could raise an issue but why would not checking in any bag raise a flag? Many people - myself included - often travel with hand baggage only.
There are various reasons whey people do not check in bags, we all know that.
Raising a flag only means that CX will pay attention and see if there is anything wrong/they need to do something about. It does not mean that they will conclude that something is wrong. In this particular instance, if they are not prepared to allow people to drop the last leg and would like to collect a higher fare as per contract, they will pay attention to those who do not check in luggage or short check. This would be common sense.