Unfortunately most everything you wrote is wrong or misleading.
The #1 reason for the difference is size is different priorities. The disk author has no reason not to use the maximum bitrate.
The recommendation for good video quality would be the HQ 1080p preset.
Topic: Compatibility issue from way that DAR is specified in MKV?
Topic: How do I do all these?
Re: How do I do all these?
Read up on the encoder presets and tunes, figure out which ones it corresponds most closely to, and pick those.
May still have some form of structural protection.
Best practice is to rip to a video file which removes more forms of protection. MakeMKV is good for this.
Topic: New System for Handbrake.
I agree PGS subs are a problem, but with no logs we don't know the subs are PGS. We've seen plenty of people muxing in 3rd party subs, or getting out their peg leg, etc.
Are you sure the credits are 24fps, not 30 or 60? I can't download the clips at the moment, but it sounds like the classic case of mixed framerate content.
Try leaving the framerate as same as source, variable framerate, and see how the scene looks.
mp4box or ffmpeg can do the remuxing for you without reencoding. They can likely keep chapters, and maybe keep subs.
Sure, I bet the developers would accept a pull request from you to better surface this error on all supported platforms.
Do you have write permission to the destination?
Topic: How does one use Handbrake(1.0.3 64bit) to encode passthrough LPCM audio?
Re: How does one use Handbrake(1.0.3 64bit) to encode passthrough LPCM audio?
Set the fallback audio encoder bitrate to 640 if you don't want the default 224.
The source bitrate is irrelevant since it's a different codec.