[Dashboard] Properly Extract and Inject references of by value panels

[crob611]

In #91567 we added some extracts to the common factories so that dashboards get proper references when saving them.

Those injects did no properly remove the references from the given state because we could have issues arise with name conflicts between two references. (Ex, a visualize index-pattern is always given the same name, so having two visualizations in a dashboard, extracting the index-patterns and altering the state, we wouldn't be able to properly piece them back together.

We should, in dashboard, handle this and maybe prefix the reference with the panel-id, or something like that, so we can pass the proper references back to inject to piece things back together properly.

[elasticmachine]

Pinging @elastic/kibana-presentation (Team:Presentation)

[ppisljar]

Agreed, if there is something unique you can prepend it with that would be perfect. If not, in expressions we use just sequential number (for example functions from 1 to x). we know that the order of functions is gonna be the same when saving as when loading so this works for us. Makes it easier however to break it if somebody would manually manipulate the saved object (which we don't recommend or support)