Subtitle settings turn off between episodes

you can enable global subtitles in settings.

Let me sort by file size so I can watch the disk gobbling files first

you can kinda deduce that if you sort by bitrate.

it sounds like you figured out a solution for yourself, already, but there's a lot of existing utilities like tinyMediaManager, WebTools-NG, Raddarr, Sonarr, etc. for doing media management. Plex is just a media server/player.