Can universities reject you based on old, irrelevant transcripts?
They can do anything they want. All transcripts must be submitted or you will find that you submitted a fraudulent application and can be rejected or dismissed because of that. Sounds like you had great success afterwards and schools do realize that people grow and change and mature. You are likely worrying over nothing. But you arent the one to decide if old transcripts are irrelevant or not, that is their purview.