SP,
The answer is simple.
It is clearance. The 3' gauge was built at the time of 2-4-0's and 2-6-0's. These were tiny locomotives compared even to the DSP&P's Cooke 2-6-0's. As locomotives became larger, the clearances didn't. The 3' gauge didn't have the benefit of a Pullman on the Lincoln Funeral Train to standardize clearances.
So, as the locomotive boilers became larger, the height and width had to conform to the clearances that were mandated when the line was built. The C&TS is not a good example of this, as there was talk as it was being built of Broad Gauging it, and the Rock and Mud Tunnels were built to accomodate this AND the Broad Gauge cars and locomotives for the Farmington Branch.
For a good example, I would refer you to Dow Helmer's Book "Historic Alpine Tunnel" where he prints a drawing which graphically shows just how little clearance even the 2-8-6T Mason Bogies had through it.
IF you want to see a good example, take a look at the rock lined cuts at the Georgetown Loop.
It is cheaper to build large boilered small drivered locomotives that fit within the clearances mandated than to rebuild all of the Platforms, water tanks, coal chutes, section Sheds, yard tracks, passing sidings. In other words anything that would be in the way of an overwidth or overheight locomotive.
Rick