In a correct transport file you would have two programs and each elementary stream would have its own PID.
But this muxer apparently does not support multiple programs, nor bitrate padding, nor PID setting, etc. So it is not useful for creating multiple program streams for broadcasting.
That's why I asked for the source code -- a reasonable request since the program claims to be released under GPL! I wanted to see if the design was suitable for extending it with those desirable features.
But it appears that Roman is taking a holiday.