If the subtitle stream contains a format other than the unique MPEG-4 Timed Textformat, you may not utilize an MP4 container. However, you can change it:
ffmpeg -i input.mkv -vcodec copy -acodec copy -scodec mov_text output.mp4
By doing this, you can include all streams, including those with modified subtitles.
The video and audio streams are not recorded; they are just copied by this command. Timed text is used to translate the subtitles.
You can also, burn the subtitles into a video using FFmpeg.