I thought I might as well jump in with a bunch of not-very-useful comments. I transcode using a... rather elaborately horrible organically-grown script that I pushed to https://github.com/nickalcock/copy-dvd-title
literally seconds ago, so it is currently totally undocumented. It *does* let me (subject to various annoying limitations) pull in DVDs or BluRays via HandBrake or makemkv or even ripped out of vlc, or directories full of pre-ripped stuff from any source, and optionally throw the lot through vapoursynth prior to encoding with HandBrake, feeding in input files that look kind of like this:
0 Fight Club :: --synth=denoise.vpy --audio=1,6,7,8,9 --subtitles=1,1,15,22,29,31 --force-subtitles=1
10 Flogging Fight Club :: --no-synth
11 Behind the Scenes: Production: Alternate Main Titles: Textless :: --audio=1,2
40 Behind the Scenes: On location
# ... etc, lines omitted ...
(The options override command-line options to copy-dvd-title, which are of course undocumented but do appear in the script: they are pulled in for each title from dvd-title.conf in all directories above the current directory, then from the top of the specified catalogue file, then from after the :: in the current title. The relationship between all these options is a flaming nightmare which is waiting for me to document it. Not all combinations are valid, not even combinations which would seem to make sense.)
The important point is that this madness means I can save a lot of space by using much better denoisers, deinterlacers, deringers etc than any available from HandBrake, with the huge caveat that this needs a lot of disk space (dozens of gigabytes minimum) for the lossless H.264 intermediates, and that vapoursynthing BluRays is... not at all fast! My preferred denoiser right now is the G41Fun TemporalDegrain2, which sacrifices hardly any detail or sharpness while slashing noisy BluRay file sizes by about a factor of five... but there is the giant caveat that this repo disappeared off the Internet last year (along with its author) so it's kind of hard to find anywhere. I'm tempted to push my fixed-up copy back to my github, since the license permits it... but honestly a lot of other denoisers, including QTGMC, work perfectly well.
So... if you have the machine time spare, do try VapourSynth or AviSynth. They can often save massive amounts of space without sacrificing quality, if you try hard enough.