There is a dedicated 72 hour transit desk at Peking terminal 3C, to the left of the foreigners' other passport desks. I handed over my passport, landing card, and a print out of my e-ticket receipt for my onward flight. I left the "Visa number" and "Visa place of issue" blank on the landing card.
The man asked me "72 hours?", to which I thought it best to reply with, "Yes" rather than try to explain it was slightly longer; he gave the eticket receipt a cursory glance and asked me to copy the flight number and departure date onto my landing card. He was very interested in inspecting every stamp in my passport for some reason, but he didn't ask me about any of them. After a couple of minutes, he stamped me in with a departure date matching my onward flight.
The chap before me seemed to be in a bit of difficulty, he was asked to stand aside and was making some urgent phone calls while I was being processed. I suspect he didn't have any paperwork with him to show the inspector.
I wondered if I would have difficulty boarding at Heathrow because of the connection being across separate tickets, not to mention being more than 72 hours, so I arrived at the airport early expecting to have a difficult conversation, and went to a staffed check in desk to discuss it. The conversation went something like this:
Me: "Hello, I'm checked in for my flight to Peking and I have the electronic boarding pass, but do you want to do a visa check before I go airside?"
Check-in agent: "Yes sir, I can do that for you now. Do you have a visa?"
Me: "No, I'm actually doing a transit across onto a separate ticket."
Check-in agent: "Well that's fine then sir. Can I help you with anything else?"
So the process has been very smooth. The key seems to be, print something out to show the immigration inspector.
Edit: I did it again today, although this time I'm only staying for twenty hours. No problem checking in at Tokyo, although this time the agent did actually want to know about my onward flight. However when I arrived at Peking Terminal 3, the dedicated 72 hour line was closed. I suspected this would be a problem, so I asked at the normal Foreigners desk, as clearly as I could, "Hello, I would like to enter under the 72 hour visa free programme", and was told to use the Diplomats line instead. Again, the chap there was very interested in printed paperwork. It took a couple of minutes to be processed.