I suppose you can modify the script to echo the filenames to output.log or similar instead of extracting tracks.
You can fix all of this by searching for all external subs and rename them appropriate to the language they are.
https://support.plex.tv/articles/200471133-adding-local-subtitles-to-your-media/#toc-3
Especially if all of the external subs are English. Find some mass/batch rename tool and rename the extensions to en.srt
or eng.srt
You will have to Refresh Metadata
after correcting all the names.