“What if this bochur has a “problem” waking up on time for Shacharis (i.e. wakes up usually after 10, 10 is early and davens biyechidus), would that change how you would handle it?”
No, it would not. If my child didn’t appreciate davening enough to take necessary precautions to ensure he made it to minyan on time, I wouldn’t focus my effort on punishing him into davening properly. Instead I would try to figure out where this disinterest is coming from.