I tried using MP4Box for this task, but it couldn't handle the M4V I was dealing with. I had success embedding the SRT as soft subtitles with ffmpeg with the following command line:
ffmpeg -i input.m4v -i input.srt -vcodec copy -acodec copy -scodec copy -map 0:0 -map 0:1 -map 1:0 -y output.mkv
Like you I had to use an MKV output file - I wasn't able to create an M4V file.
