Interesting. The last few flights I was on there was an agent from the GS check-in that thanked me as I was boarding. I also saw her on board during the boarding process, maybe she was talking to the flight attendants to identify the GS passengers? Because once I was on board, they definitely offered me the snack box and seem to know I was GS.
If there are no manifests, maybe they are doing it manually and notifying the FA?.