I think for now the system will only cancel a duplicate if both flights are scheduled to be in the air at the same time. That's a conflict the customer cannot dispute.
I doubt they will pick a threshold that low. I think it would be at least be double the MCT plus the return flight time. That might be difficult
to program in the revenue integrity system so I bet they will just look for multiple flights from a single origin in a calendar day.
Can you book a 4 segment segment trip between two airports in one PNR? I doubt RI would look for duplicates within a single PNR. I know booking multiple segments in a single PNR is not ideal for a number of reasons but it would defeat the RI mechanism.