For people who cannot hold their head up the airport wheelchairs are unusable and so they have to be given their own at the plane. It's aleays happened for us and I was under the impression that this was the case for all wheelchairs and the airport ones are just for people with reduced mobility but not travelling with their own wheelchair.
Either way let them know in advance that you will need the chair and remind people throughout. You should get it before getting off and just wait on the plane until they let you know it's there.
However. Things can and will go wrong and so pack for the worst case scenario so you can pop him in the airport one with headphones, tablet, weighted blanket, whatever gives the best chance of him making it through the airport.