I suspect that Tom is right. The SPC was built as a narrow gauge line, but to very high standards including very light grades achieved by use of lots of tunnels (9 on the original line, two over a mile in length) draw bridges where needed (they had 4) standard gauge ties and 52 lb. rail (same weight as CP was using at the time)
The line was sold to SP in 1887, and dual gauging was well along by 1902. The big obstacle to the lines standard gauging were the long tunnels. In 1903 the SP started to pull NG equipment from the line for the Nevada & California, to deal with the Tonapah gold boom, resulting in embargo’s on direct narrow gauge shipments from the Santa Cruz and Boulder Creek areas, requiring the traffic to move via standard gauge via Watsonville. The 1906 earthquake closed the line which reopened as standard gauge. But the narrow gauge equipment was used to rebuild the line, and according to some reports the tunnels were dual gauge during the rebuilding.
So yes, there were dual gauge tunnels of great length, but they long ones probably never saw regular service as three rail tunnels
Randy Hees