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

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### 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 @lantiga @borda @mauvilsa

Start by defining test cases for argument linking between CLI inputs and config-file inputs, as described in the issue, and use them to identify the inconsistent cases. The work is done when the behavior is consistent and a documentation page explains the Lightning CLI-specific nuances beyond jsonargparse.

Written by the indexing model from the issue text.