I don't think it's fair to expect CA to be aware of MPO benefits on CX flights. This is essentially expecting all check-in agents to know every single airline's benefits for passenger on each airline's flts. You had the option to either short check the bag or pay the full fee. I remember reading that CI will reimburse their members in such circumstance (or at least CI used to), but either CX doesn't do so or at least doesn't publish this benefit.