ADPPro's YouTube video How To Stitch and Blend Bracketed Panoramas shows how to reuse the setting from one set of images having a normal exposure and apply the exact same transformation on the second set where the only thing different is the exposure. He does this so he can do his own luminosity masking stuff in Photoshop. In the video he uses PTGui, but I would like to do the same in Hugin if possible.
If I understand correctly what you are trying to achieve, you can just load all of the bracketed exposures into one project, do all required optimizations as you wish, and in the "Stitcher" configuration under "Layers" select "Blended layers of similar exposure, without exposure correction" (may vary somewhat for different versions). This should give you one independently stitched image for each exposure level, possibly in addition to other output files.