If only the container was an issue, you would have a direct stream which doesn’t impact quality, it just repacks it in a container that is compatible with the client.
You can see the transcode reason on the dashboard by clicking on the i symbol. Start playback on android TV, open jellyfin on your phone and you should see the transcode reason.
And because they are such black boxes, there’s the sector of Explainable AI which attempts to provide transparency.
However, in order to understand data from explainable AI, you still need domain experts that have experience in interpreting what that data means and how to make changes.
It’s almost as if any reasonably complex string of operations requires study. And that’s what tech marketing forgets. As you said, it all has to come from somewhere.