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<p>That isn’t what “penalize” means here. The question is whether there are any possible circumstances where those who accomplish more score lower than those who accomplish less. In your example, a student’s score will go down if he accomplishes more by enrolling in the additional class and receiving an A-minus, or any grade below the maximum possible.</p>
<p>Your example, like some of the earlier ones here, is “valedictorian-centric”, focusing on the specific penalty of drops below 4.0. As I mentioned, you can’t have a system that always gives flawless grades the highest score without introducing other distortions and penalties. However, even if we only care about those who can attain perfect grades, they too are penalized for taking extra (unweighted) courses under any system that averages, because their score cannot rise, and their risk of reducing the score goes up, although they are doing more by taking those courses.</p>