Your son sounds quite capable academically.
I would just toss a few ideas out there for him to mull over as he goes through this process.
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Why is he looking at schools like like NESCAC for sport if he really wants an UG b-school? Is it because of sports? He should really only be looking at schools for sport that are also academic fits. It’s really easy for athletes to get excited about schools that want them. It’s also easy for kids who LOVE their sport to minimize the role they want it to play in college because they are considering schools where they can’t play. Where/how does this fit in the equation for him?
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Look at overall distribution requirements in the programs he’s considering. Make sure those are all represented in his HS curriculum. For business, that is likely to be well-rounded and to include FL… He may even get lucky and get credit or placement for an AP exam. It’s fine to take an easier AP, btw, with the STEM rigor he has. Don’t sweat that.
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Encourage your son to try to really tease out how he feels about some of the other points you have mentioned. Why does prestige matter to him? (He can have it, btw, but he should think this through. What will be different about those programs from others and what does that mean to him?) What does he actually enjoy? Kids who feel they should have a certain college outcome because of the work they put in are saying they found it a grind. If they’d just loved the learning for its own sake, college admissions owes them nothing! He may be a less life of the mind person and the practicality of b school could be a great fit. But in particular, the comment about not getting to take an elective he wanted suggests that he has genuine intellectual curiosity outside these foundational areas. College can feed that - try to find places that will keep that open. There is a ton of opportunity in business for people with strong STEM backgrounds and if your S wants to continue to build on that, make sure he can. IME, the STEM folks can master biz skills easily (and businesses hire them). Not always so easy the other way.