I’ve only used Encore. I’m not sure what a better or easier option would be (there aren’t very many options in the first place).

Most software will probably try to re-encode something like Despecialized, as they detect or assume that it is not BD compliant. If that’s something you can’t get around within the software itself, you can just author the disc and then replace the main video using multiAVCHD. People have posted a guide for that around here before, I think.

As you’ll see with njvc’s discs, Encore (and probably anything else) will also limit your audio track count. With multiavchd, you can then go ahead and add all the extra ones you want. You’ll just need to use your remote to access them instead of the BD menu.