I believe that the system actually locks the user out, the check-in agent can't make any exceptions as a result. I've seen this done at boarding when I asked to change seats, the agent physically crossed out my old seat and wrote another because she wouldn't be able to change the seat in her system. This is in aid for EK's dispatch/pilots to be able to receive the final weights so that the flight can depart in time. If certain time constraints aren't met then it screws up other time constraints down the line. If you're without a bag maybe online check-in is the best option?