Clara survives the fire in the cellar, even though the only entrance is inside the house which is burnt completely to the ground. The fire would have consumed most of the air in the cellar, which was entered only from inside the house, leaving Clara to die from either asphyxiation or carbon monoxide poisoning.
The Allen house, 2 stories high with an attic, is burned to the ground, but leaves no appreciable ash or debris on the cellar door entrance that would prevent it from being opened.
Isaac's headstone sets the year as 1878. When Pea Eye is looking at the recovered bullet, it has a copper jacket. However, copper jacketed bullets were not invented until 1882.