HandBrake

Hi, i did some reading on the forum and found that video-pass through is not an option for HB

So can't there be an option where you only select an audio or subtitle file for encoding within a container like mkv?

For MKV, mkvtoolnix has tools to do exactly that. You tell it which tracks to include in the output file.

No, for the same reason as no video passthrough: HB's architecture is predicated on video encoding.