I think this is where OP is seeking help - not necessarily concern about how schools will evaluate but how this student’s profile will be seen.
As they note, some schools report above a 4.0 - so are reporting a weighted GPA - so how do they, on their own, figure out where their kid sits.
That’s why I suggested a chance me - as well as talkingt to a counselor - so we can help them determine how they might fare - after taking into account rigor, test score, ECs, etc.