I’ve never used that option, so unsure how it works.
Regarding remuxing, if you’re good with scripting you can try using ffmpeg via CLI.
See my post here regarding copying all tracks.
Also see this post which mentions optimizing the file (mine doesn’t).
Between the two you should be able to find a command that copies all tracks and optimizes the file.
I’m not sure how much embedded metadata is copied, so be sure and test if your files have embedded metadata for actors, directors, etc.
