renaming the files

Can be automated

grouping them into folders by franchise

Should be managed in database rather than filesystem, and automated

remuxing videos so they would only have one audio and one subtitle file, reencoding videos that I considered bloated, reencoding videos that had flac or 5.1 audio to opus stereo

Waste of electricity and requires you to backup the file itself rather than a torrent, as you no longer have exactly what others have. Also a minor point you will kick yourself if you ever buy a surround sound setup and/or discover the wonders of headphone virtual surround

putting all my files into a spreadsheet along with other information

For any media category there almost certainly exists a database system that can do this for you automatically. You mentioned anime, in which case an example is Shoko

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tl;dr you're complaining about a problem you created, and solving the problem by scorched earth-ing the entire problem