My thoughts:
It seems the fare is technically a return PEN-SIN (on the way in with a connection in DXB). In our case, the time between arriving in SIN (from PEN) and leaving SIN (to DXB) is 1 hour and includes a plane change. It's technically when we start our return flight already. Therefore, my understanding is that one should therefore check in online for the SIN-DXB-PEN flight before leaving PEN already to avoid being treated as a no-show. As well, I wonder if you could check in luggage in PEN for that reason. You cannot always check in luggage for your outbound and inbound flight as the same point. Any thoughts?