In this case, as I mentioned, the HDR merging will be a no-op (it will simply copy the input to the output). 
Is its presence that much of a problem? I personally use the aforementioned workflow even for “standard” panoramas.
I will have to think about it, but thanks for the suggestion. 
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My experience differs a lot. It can’t be a no-op if it produces ghosting on overlapped areas where regular old stitching does not. Maybe I was doing something wrong.
Is it possible that maybe the images were accidentally assigned to the same stack?
Yes, I revisited my panorama workflow and Hugin was indeed assigning images to the same stack.