I haven't figured out the balance between using renaming software (I've tried the free version of Filebot, but it has horrible latency for some reason.), and being able to remain a contributing member to certain media communities.
My solution to this has been symlinks. All the media files I download maintain their original names and structures so they can continue seeding, and I maintain a separate folder structure that complies with Jellyfin's naming conventions. All the files are just symlinked so they don't take up any additional space, and I have a couple small scripts to check for missing/broken links.