1) You go in after feeling confused and have a headache after falling from a skateboard with no helmet. The ER sends you home not having checked anything or any notes to watch out for because they think you're too young to have problems from a fall (despite many young people having problems after a fall each year). At home you die because of a brain bleed.
vs.
2) You go in after feeling confused and have a headache after falling from a skateboard with no helmet. The ER runs some tests, sees the problem, and prescribes the best course of treatment given this information. Despite this you still die or have lasting effects on your brain.
Despite the doctors not fully remedying your problem in both situations only situation 1 involves negligence for a malpractice claim because the problem isn't the outcome, it's the quality of treatment not meeting the minimum levels. Flip the scenario specifics back and what GP is saying is that it isn't considered negligence to say "you're under 40, you're fine, go home" instead of "you could seriously be having a problem. We should put you on a statin and talk over the risks/symptoms of a heart attack" because the standard of care (sort of one measurement for what's a negligent treatment action) says the calculator defines the appropriate treatment and the calculator doesn't even work for those <40. What GP is not implying is doctors are negligent just because you still had a heart attack anyways.