There is padding in the schedules that may help. But if you find that your incoming leg is delayed, you can probably make a case to an AAgent to reroute you. That doesn't help when the available seats may be gone or left with less desirable choices, though. If you can find AA documentation that states JFK Domestic -> International MCT that is more than 41 minutes then you may be able to call again and point the agent to their company's own policies.