SAT/ACT on transcript

Let’s say that there’s a major discrepancy between one’s ACT and SAT scores. Let’s also say that this applicant’s school decides to put these scores on their transcript. Will elite colleges look at official score reports or will they look at transcripts as well for scores? Furthermore, will they consider both scores or will they only look at whichever one is comparatively better?

My nephew asked his school to take off the ACT listed on his transcript (he did better on the SAT) and his school did. There is no requirement that scores be listed on transcripts.

If the transcripts were already submitted, do you think it would impact chances?