I was actually on a local Church board until a few months ago, filling the position the pipe is named after to some degree.
Coincidentally it's my favourite kind of pipe too. The biggest reason that I prefer the Churchwarden, almost true to the joke posted above, is to keep smoke away from my face. I'm pretty much always smoking outside and unless it's a dead calm day even the slightest breeze will often waft the smoke into my face, stinging my eyes and nose (I never retrohale, my nose gets stuffy enough as-is).
(this is also the case because I primarily push smoke back out through the pipe after drawing, only occasionally letting smoke out between my lips)
On the subject of a long stem providing "cool smoke", I have a feeling that statement is mostly just based on the vague assumption that pipe smoke is hot to begin with.
Smoking a short pipe with an open draft, such as a Missouri Meerschaum hardwood pipe, I do notice the smoke feels warm compared to a Churchwarden, but even in the worst case I could hardly call it "hot".
I won't believe that pipe smoke has any significant amount of thermal energy until someone gets thermometer to say otherwise.