Many of those "poor 'holistic' qualities" can be code words for discrimination. "Social skills" for neurotypical, "leadership" for attractive, "athleticism" for not disabled, "disposition" for obedient.
Even if you're right and extremely high SAT and grades are correlated with neurodiversity, physical problems, or rebelliousness, are those qualities colleges should be discriminating against?
There's certainly a heap of evidence of discrimination against neurodiversity, physical problems, and rebelliousness. It's certainly been talked about enough. If you're not aware of it that's only because you've chosen to ignore it.
Even if you're right and extremely high SAT and grades are correlated with neurodiversity, physical problems, or rebelliousness, are those qualities colleges should be discriminating against?