Looks to be working fine here, although maybe a little counter-intuitive.
The default settings has Deflicker percentile @ 50% and Deflicker target level @ -4 EV. This says, find the 50% brightness point of the image and place it at -4 EV.
So imagine you shoot a clear sky with ETTR, the deflickered image would have a brightness level around the midtones. Because a clear sky has little dynamic range, 50% brightness represents almost the entire image, and so deflicker would place this image @ -4 EV. In other words, the deflickered image would look dull because it is being rendered as a midtone instead of a highlight.
Now imagine that you do not change exposure settings, but pan the camera so that it includes the sky, but some darker content also. Here, the 50% brightness point is probably somewhere between the sky and the dark areas, so the deflickered image probably won't change much, because the 50% brightness point of the image is already around -4 EV.
Now imagine that you do not change exposure settings, but pan the camera so that it only includes very deep shadows. Here, the dynamic range is also probably small, but the image has been shot as a shadow. So the 50% brightness point is somewhere in the shadows, and hence, the deflickered image will be brighter since deflicker will push this 50% brightness point to -4 EV.
My current panorama method of choice when shooting a large dynamic range scene is using dual ISO. Since you can shoot around 12 EV of useful dynamic range with dual ISO. So I will generally frame the brightest portion of the image first, ETTR this @ ISO 100 with dual ISO enabled and then dual ISO will take care of the darker areas of the panorama. Since exposure settings don't change, it's very easy to exposure match the images. Just enable the --same-levels option when processing the dual ISO images, and ensure the same WB.