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For change the encode you need to edit the code directly from file components/com_community/libraries/video.php, look at command <i>$cmd[]</i> you can put your encode from there.
But, in another hand, your issue actually valid bug, because we also valid bug which the video can be played but just audio no of images video as well
you can put your own command, actually we use the default encoder from mp4 library with libx264 and aac, if you want add your own encoder code you can put it like this :