Note that when you decide your transcoding settings, only some container formats (muxers) can support some codecs-look at streaming features compatibility matrix to see which supports what. In the GUI this is called 'keep the original track' (I think).

If your input streams already matches the encoding that you desire for your output stream, then you don't have to transcode at all (just leave out the transcode settings on the command line, and it will thence not transcode).

5 Non-Interactive Batch Transcoding (Windows).3.2 Completely non-interactive transcoding.