[AstralStorm]

Sounds like there's a lack of feature in the CLI tool. You will have to write your own, pick a language and it probably has enough of low level ffmpeg bindings to do this. The library supports streaming reads and writes very well, though you may have to provide a custom reader callback or use the old loop APIs.

[BubRoss]

ffmpeg from the command line is very powerful and people use it for what is being described here all the time. Why do you think it is necessary to have to resort to the library and API?