Ok, looks like the problem is completely with the Gamma setting.

In my first test above, I thought the settings were the same with the manually setup scene, but didn't realize Gamma was checked in the firefly auto settings. When I uncheck Gamma, The shaders and displacement maps are vivid and obvious. Correction also, the shaders and displacement maps aren't being ignored, but they are definitely subdued. The top image is PPro no gamma, the bottom is gamma check with default of 2.20.

So, something is clearly different. I would NOT say the gamma version is a better render.