Yes, that's a tough problem – you have the option of

1. Editing the three bracketed nadir shots separately in GIMP (bad idea, because you'll never be able to rubber-stamp exactly the same pattern in each exposure).

2. Creating tone-mapped stacks of each individual tile, then editing the nadir shots in GIMP and stitching them in Hugin (not recommended, especially if you're using tone mapping operators such as Mantiuk06 and Fattal – they will take matters into their own hands and really muck around with the exposure, particularly at the edges of the image, so when you go to stitch the image, you'll get all sorts of patches with dissimilar brightness).

3. Stitching all the images (including nadir shots) in Hugin, leaving the nadir shots un-edited, saving it as a low-dynamic-range (8-bit) image, and then editing out the tripod in GIMP. Depending on the projection you use, it might be quite difficult to edit out the tripod – think about how huge and stretched Antarctica is in most map projections! If you're doing one of those 'little planet' projections, though, it should be no trouble at all.

With the open-source tools at your disposal, I'd go with option 3. Unfortunately, every time you output a new version of that pano from Hugin, you'll have to take the 8-bit image and edit out the tripod. Kind of annoying, but it will allow you to maintain the HDR integrity through most of the workflow. Ideally, you want to tone-map it as late as you can.

In Hugin parlance, 'high dynamic range merged stacks' means an HDR image – or rather, each bracketed stack (three low-dynamic range images) is exported as a separate HDR tile.

In Hugin, 'exposure fusion' creates a low-dynamic-range tone-mapped image using an HDR image (that Hugin creates and then throws away). Hugin's tone-mapping is pretty good, although I find it creates pretty low-contrast images.

The purpose of Luminance in this workflow would be to play around with different methods of tone-mapping. I often output the stitched pano as an HDR image (in EXR format) from Hugin, sidestepping Hugin's tone-mapper, and then play around in Luminance. Landscapes can have a lot of contrast between highlights and shadows, and it sometimes takes a bit of effort to get things balanced. My favourite method is:

1. Tone-map the image with Reinhard or Mantiuk08, and save that JPEG. This will give you a low-contrast but realistic base image.

2. Tone-map the image again with Mantiuk06 (contrast 0.2, saturation 1.2) or Fattal and save that JPEG. This will give you an unrealistic image that has strong local contrast (details are enhanced) but low overall contrast (shadows are lightened, highlights are darkened).

3. Load up both images as separate layers of the same image in GIMP (image 1 on the bottom) and play around with the transparency on the second layer until you get a pleasant looking image. You might want to set the second image's blending mode to Overlay and knock the opacity back to 25% for starters.