Multichannel Audio

Dolby Audio Files including Atmos.
Multichannel Audio.

I don’t understand what you are asking. There is an option to COPY audio. I assume that means any and all audio streams.

From what I see it Only does 2 channel Audio.

And if your source has multiple audio tracks it won’t carry those over, either. You also lose subtitles and chapter markers.

What I do is use my video editor to replace the video stream in the original with the enhanced video stream.

Exactly. Or, if you like me don’t use a full video editor for most tasks, MKVToolnix will do that job as well.

OTOH, some of the enhancements, like slow motion, change the duration of the finished video and would throw off audio sync. Not sure how that could be dealt with internally without bloating the app into a video editor.