This is probably quite obvious, but I had been wondering about it for a while and only got off my butt long enough yesterday to figure it out.

Hugin's Enblend and Enfuse can indeed be run multi-threaded. On linux, the programs are simply invoked as enblend-mp and enfuse-mp instead of enblend and enfuse, respectively. Hugin can be set to use these from the preferences tab.

Real results - a panorama that might have taken an hour or more now takes just a few minutes. (On an i7-4960x).

Unfortunately, I was not able to successfully use the --gpu option for enblend-mp (also set in hugin, or invoked from the command line) - I have no idea why, since it should be supported and all that, and my card (R9-280) is recent enough. It would start to work, but then fail with some signed integer overflow / out of bounds conditions.