There should be a way to replace i.e. the visual track in an existing container with syntax following the -add option, i.e.
mp4box -replace 1 new_track.h264:par=none existing_file.mp4
I believe this is equivalent to MP4Box -rem 1 -add new_track.264#trackID=1 existing_file.mp4
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I believe this is equivalent to
MP4Box -rem 1 -add new_track.264#trackID=1 existing_file.mp4