This is an old thread, but I'll share my technique after some trial and error and a bunch of reading.
use AnyDVD to rip (I used a LG BD-R/hd-dvd unit off ebay)
then use clownBD to demux the HDDVD video to a temp folder (dont' use TSmuxer yet)
(I picked NMT option on the first screen and then LPCM and AC3 on the following screens)
run tsmuxergui separately and grab the files from the temp folder and load into the input window.
grab: vc1 file, ac3 file, w64 file (if you want LPCM option), True HD file if needed, and an srt file you can get from a subtitles site.
edit the chapters.txt file and remove all but hh:mm:ss and separate them by ; So it'll look like 00:00:00;00:05:00;0008:30 and so on. (no semicolon after the last entry). Copy and paste those times into the blu-ray custom chapters list section
pick blu ray folder option and a path.
execute. You'll get a BD disc structure. You can make an iso from that structure and burn it. The burnt disc played in my 4K players (samsung and philips) Watch the file sizes. I was able to get all onto a 25GB disc. One or two I had to leave off LPCM as the resulting ISO was over 25GB
I found this works all the time for me. The sound is fine, the subtitle works and the chapters work.
I converted 14 of my discs to 25GB BD-R. Makemkv was too choppy due to pulldown problems and the subtitles didn't work all the time.