Wow a lot to go through here but I will try to keep it as simple as I can.
Version control ?
YES of course ! And an extra triple YES YES YES ! Is the answer to using version control. This is one of the most important reasons to use linking. Along with keeping scene data complexity and size manageable of course. The version control aspect of linking is absolutely vital. In most animation pipelines the schedule and process will overlap. There is not normally ever the luxury of waiting on somebody making all the models and textures to be perfect and nice before starting the rest of the process. As in scene layout, Animation blockout and final animation.
Also version control is needed and very important to have with the rigs and other complex scene set ups like 3d effects elements. Most often rigs will need tweaking in production or take more time to finish and fine tune once animation has already begun. With linking the character rigs will always be updated across all scenes automatically with normally no disruption at all.
So if you are on the animation team and see a problem with the rig not being able to work for a particular action you are animating you talk to the animation TD. A lot of times the animation TD was me. Then I add the rig update or improvement that afternoon. If it is not an emergency fix I would wait until the end of the day or early morning so as not to risk sudden disruption for anyone in the working day. Then I update the rig on the main server. In studio practice we call the process of adding an asset or updating an existing rig or asset to the main server ( Publishing ) So you will commonly have multiple incremental versions of published assets as a production rolls along.
The next morning when you open your same scene that you saved the day before the rig will be updated and hopefully the improvement you asked for will be there and working well. But not only for your scene. Everyone else will be automatically working with the same updated and improved rig too. Also all of the scenes with that particular character will have the updated rig on opening. Sometimes a rig update might break something else in another scene. In that case the published rig will be rolled back to the previous version while the new problem is fixed. Then the rig can be published again as another incremental version. Etc etc etc.
In this way everyone can work on the scenes without needing to worry if the assets are the right or latest versions since that all happens automatically. I think this is just as important however if you are working on a project solo or setting this up for a studio team. In both cases you do not want to be distracted by the assets in your scene if you are animating lighting or setting up for render. You want to be able to focus on each task fully without extra unnecessary stress and complications.
As for how to order the files and what to link to. I will look at the diagram you mentioned and make it another post since this has got very long again. But yes. Always give yourself the option to exercise version control.