You can easily set it to keep the default Japanese language and English subtitles for the anime and English audio and subs for everything else. I created 2 profiles. Main profile for everything non-anime to keep english audio and subs and an anime profile to keep Japanese audio and English subs. It remuxes everything, keeps it all in its directories and doesnt change filenames or anything, just removes unwanted tracks and subs and library remains intact in Jellyfin/Plex.

This is great. Set it up in a few minutes and just started and already saved a couple GB in just a handful of movies. Tested the conversions and it worked like a charm. Thanks for this, had no clue this existed.