I explain that very easily - AOs are NOT looking for perfect score kids. When I’ve spoken to AOs at both my kids school they often talk about the top 4/5 things they are looking for in a kid and perfect grades or ssat scores never come up. They are often looking for kids who are engaged in things they love beyond academics.
My guess is that yes, lots of those kids with perfect scores had something that was a red flag. A teacher mentions in a rec that the kid seems very focused on getting a perfect grade - red flag. Kid goes on and on about their accomplishments - red flag. Kid can’t look an ao in the eye or talk about anything in a conversational way - red flag. How many kids posting on cc rub you the wrong way because they clearly don’t know the meaning of humility? Those little impressions surely matter. Boarding schools are building a community and they are very aware that the kids actually have to live together 24/7, they are weeding out the kids that every other kid in their dorm is going to hate.
Frankly it doesn’t seem confusing to me at all.