Embedding subtitles in the video and also keeping the file is pointless and it results in 2 identical tracks for the same video.

The default behavior of youtube-dl is to keep the file if not embedded and delete it if embedded, this is smarter because the -k flag can be used if someone wants to embed and also keep the file, but there is no flag to automatically remove the file once embedded.

Maybe adding a flag like --keep-subs-file would solve the problem for those few users who might want both, but the default should be what youtube-dl does, keep the file if external subs or embed and delete.