This one is from 1959 I believe. Looks like one tunnel for the train and maybe another one for the Painted Desert backstage access? Looks about right since the Fantasyland skyway chalet is just off to the right of the painted desert tunnel. Just like the current demo pictures seem to show.
Thanks for these pictures--they fill in some details for me that I could only infer were there. If you were on the other side of the tunnel in the color picture of the Painted Desert, you would see three tunnels. The one in the color picture runs NE to SW and is now paint storage. In the B&W picture you can see the SFDRR tunnel next to it that runs W to E. Behind the train in the color photo is the tunnel that now runs from FL Theater to Big Thunder Trail, and under the back of the old Skyway station.
My rebel spies are speculating how much of this is about to be demolished along with the Skyway Station, including all three tunnels.