Auto add subtitles into the MP4 videos?
You might use mkvextract to extract subtitles:

brew install mkvtoolnix;for f in *.mkv;do set $(mkvmerge -i "$f"|awk -F'[ :/)]' '/^Track ID [0-9]+: subtitles/{print $3,tolower($7);exit}');[[ $1 ]]&amp;&amp;mkvextract tracks "$f" "$1:${f%mkv}$2";done

Then use the external subtitles with the mp4 files.

The mp4 container doesn't support srt or ass subtitles, but it does support ttxt (MPEG-4 Part 17) and VobSub (sub and idx files). I couldn't get ffmpeg -i input.mkv -c copy -scodec mov_text output.mp4 to work though, or at least the subtitles weren't displayed by VLC or QuickTime Player.