Your issues with sonarr seem to entirely be based upon a lack of understanding. For one thing it seems like you probably didn't set the show to the anime format which detects absolute numbering. And beyond that, the rename tool provides an interactive interface where you can easily verify and adjust the renaming. Not to mention, sonarr's purpose is primarily retrieving and indexing content. Content which usually adheres to a standard naming already. Renaming existing content is a secondary function and is the wild west when the files might be in whatever nonstandard naming convention the user thought up.

Since it's renaming files, it has to keep the original file to seed the torrent. That's completely understandable but I wish there was a way to have it wait until ratio/time limit before renaming. It would save hard drive space to allow that.

This is where I can really tell you just don't understand the program. One of sonarrs primary features is hardlink management. When a torrent is done downloading, sonarr creates a hardlink from the torrent file to the proper location in your media directory and then renames that hardlink. There's no additional storage usage. It wouldn't be helpful to wait for a torrent to finish seeding to rename it because in the mean time it wouldn't be picked up by Plex/Jellyfin because your torrent directory is (or rather it should be) separate from your media directory that Plex/Jellyfin sees. And additionally, another primary benefit of sonarr is that it allows you to permanently seed torrents while also having nice naming. In which case your file would never be renamed if it waited until it was done seeding of course.