Eugene Sledge, in his book With the Old Breed: at Peleliu and Okinawa, includes a roughly drawn but detailed diagram of the bunker itself and gives a very detailed explanation of the way it worked.
The bunker had been specifically designed to withstand not only enemy fire on the outside but also to protect the soldiers inside. Inside there were a series of rooms or chambers that were placed so the entryways (or doorways) were staggered so they did not line up. This "baffling" system would prevent grenade fragments from shooting into other rooms in the bunker. When Leydon and Burgin drop the grenade in the vent on top the grenade probably only affected troops in one room. The Sherman tank that fired on the bunker likely did more damage, however the ground assault by Sledge's team and the flamethrower trooper finished the job.