Providing you're don't need to strictly adhere to the chapters, I found a solution. Download a free converting program called DVD Flick, and then find a DVD ripper.
Go through the process of reauthor, but stop after combining the movie audio and the rifftrax audio. Rip the DVD. Using DVD Flick, add the ripped file, replace the ripped audio with the Rifftrax audio, and convert/burn. It's how I get around IFOEdit's periodic screwups.