Grades and test scores are only part of the application credentials. Colleges look at EC’s for good reason. They may reveal what motivates the applicant, but more importantly perhaps they may reveal the applicant’s interests and commitment to work hard on things he’s really attracted to.
My best case in point is my son. He got decent high school grades (about a 3.6 average) in a strong curriculum. He got extremely high SAT scores. And he had outstanding achievements in EC’s that demand thinking ability, for example he was a state champion debater; he won statewide awards in journalism; he was 2nd in the state in a math competition. Competitions excited him. Schoolwork not so much.
He got into many fine colleges; attended UChicago.
So my basic advice in this case is to focus on performance and achievements and qualifications overall. You don’t have to explain away his grades. It’s likely that his letter-writers, if well chosen, will also emphasize his special talents and achievements.