What seems to have happened here is that the OP's colleague had boarded the aircraft in question, having already shown the passport, and then handed the bag over for checking into the hold whilst on board. So typically there wasn't enough space for his bag so the cabin crew invited him to put in the hold. He would have left it in the front galley, where it would have got a manual tag and then someone from GGS would take down to the apron and into the hold. Presumably this unexpected set of events led to a senior moment.

Edit: another scenario is that the passenger took advantage of the priority boarding at the gate, or was pre-tagged, and there the procedure would be for the passenger to be onboarded via FLY, thereby showing the passport, and only afterwards to leave the bag at the top of the bridge.