Impove how argument passing via CLI and config file is handled in regards to argument linking

[MrWhatZitToYaa]

Description & Motivation

I was working on several larger projects and I noticed that the behavior or argument linking is somewhat arbitrary. I propose to make this more consistent to avoid user confusion. Furthermore I propose to write a documentation page for this, since the one from jsonargmarse is not sufficient due to some nuances in combination with lighnting CLI.

Pitch

I would like to make the behavior of passing arguments via cli and config file more consistent in regards to argument linking. There are several aspects to this that I still need to figure out. I will start by writing test cases and update on the go.

Alternatives

No response

Additional context

No response

cc @Borda