how to pipe:/// through a .sh or Python script, or use some sort of setting files with FFMPEG
I didn't find an actual answer, more a work around. As this was all part of a bigger, involving plex, I found a proxy (xteve) that includes ffmpeg transcoding, and I can set the options for ffmpeg.  That is good enough for what I was trying to do.

Hope this save someone else a little time.