Sure.

The Despecialized Edition contains an M2TS file, which is the video and audio all "muxed" together into a single file. (This is from memory, I may be skipping some important steps, so you may need to experiment) Open that file on tsmuxerGUI, and then add the 720p SUP file from Project Threepio. Then set the target to either AVCHD or Blu-ray, depending on what you're making, and that will create a new folder structure. Then you can use ImgBurn to actually put this on a disc. Some of this is explained in the Project Threepio README.