In case anyone comes upon this and needs to convert MOV to MP4 using FFMpeg, the correct method is:
$ffmpeg = FFMpeg\FFMpeg::create();
$video = $ffmpeg->open('path/to/movie.mov');
$format = new FFMpeg\Format\Video\X264();
$format->setAudioCodec("libmp3lame");
$video
->save($format, 'path/to/movie.mp4');
Answer found here