I think for muost public transport tunnels it normally involves an escort fore and aft and closing the tunnel to other traffic - if the tunnel is seperate from the one in the opposite direction than only one tunnel is affected
You occasionaly see hazardous cargoes parked up near the entrance to major road tunnels (eg Liverpool, Tyne etc) with an escort waiting for an opportune time to go through
Oddly I've never seen one at the Hindhead Tunnel on the A3 so maybe they just sail straight through.......