The magnificent @patdavid has tried the focus stacking: https://patdavid.net/2013/01/focus-stacking-macro-photos-enfuse/
Frankly, the HDR function of darktable doesn’t work well for me. There are several plugins to try and deal with this, but really, you should try Luminance HDR or HDRMerge for HDR merging.
Hugin can also give you an HDR file, but if you want HDR, I find the other two programs listed to be better. Hugin will give you really good exposure blending, which blends your bracketed shots into one LDR tif file. I like the exposure blending, as it usually yields a fairly natural looking image.
Another option is to pull your bracketed shots into GIMP as layers, then use luminosity masks to manually blend your images together. Again, @patdavid has you covered: https://patdavid.net/2013/11/getting-around-in-gimp-luminosity-masks/