Everyone assumes that the tunnel interior is stable. Not necessarily so. There supposedly isn't any really solid rock in the whole length of it. Before construction started in 1880/1881, the railroad owners and the contractor expected it to be solid rock all the way through. The contract bids allegedly reflected that. After starting, they discovered, quickly enough, that it was loose rock which had come down from the mountains on each side of that area over a period of thousands of years. Look at the photos of the outside areas in he broad portal areas and you'll see what the rock was really like. Just compressed together a bit. Such loose rock often is called "scree". Pretty common in Colorado.
The contractor had to stop, or turn to other things, and order redwood timbers and heavy redwood sheathing from California. Full tunnel work resumed as soon as the wood started arriving. Look at the interior photos; it's timbered all the way.
Redwood is known for its resistance to rot, "dry rot" in particular, and to fire (such as embers from wood burning and coal burning locos) but it is NOT nearly as strong as other woods. That's part of the reason the Tunnel timbers are so large. In addition, look at all the white places that show up on all the timbers in any interior photos. That is a fungus which grows on untreated cut redwood lumber. As any owner of an exterior redwood deck knows, that fungus will break down the redwood over time and cause it to lose its strength. The fungus does not grow on redwood under water but thrives on redwood that is almost continually damp but still exposed to air. My second story redwood deck had that fungus growing on its underside (rainwater drains through the deck; decks usually are designed that way). It was only 15 years old but we replaced the deck surface with Trex-type synthetic planking. The redwood deck was starting to become dangerous to walk on. Of course, our redwood planking was light, relatively thin material, not anything like the heavy virgin redwood used in Alpine Tunnel 130 years ago.
BTW, virgin redwood lumber no longer is available at any price. The remaining virgin redwood trees in Calif. are all in parks or otherwise conserved. I live in part of the redwood county only 30 miles north of SF across the GG Bridge.
So don't let the APPARENT appearance of the timbering fool you. There have been far to many cave-ins, large and small, in that tunnel for the timbers to be anywhere near as strong as they look.
Best regards, Hart Corbett