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I found an even easier fix. Once you have a DRM removed copy, go into BDMV\STREAM not PLAYLIST. From there use the files 00005-11 for disc 4 and mkvtoolnix can just use them files fine with both audio types first try.

So for Death Note i figured out a work around, i hope it can help somebody else seems you can extract the episodes by loading the playlists at BDMV/PLAYLIST into MKVToolNix after making a backup without the encryption, the seem to be 00005.mpls - 000011.mpls on each disc are the episodes, MKVToolNi...