With all this, it is worth while to make sure you understand the underpinnings of SketchUp’s system of “components” because the term is used loosely used to cover the whole concept and the actual bits in play in various operations might not be what you think. This reply may be too technical or TLDR, but hopefully it will help you to appreciate what is going on…
The heart of a Component is a Component Definition. This is like a template that spells out what is in the component. Component Definitions are like abstract objects waiting to be made real. They are what you deal with if you open the Components window.
What you see in the model is an Instance of the Component. That is, a concrete collection of stuff assembled based on the instructions in the Component Definition and placed at a specific location, orientation, and scale in the model. You can pull a new instance of a Component out of the Components Window and drop it the desired place in the model. Or you can create a new Instance by copying an existing one in the model.
Each Component can have any number of Instances placed in the model - including none.
That last point causes bloated models if you experiment with a lot of Components and then delete the ones you no longer need. You actually delete Instances. The Definition remains in the model’s collection. Do that a lot, and you can have a lot of memory being hogged by Component Definitions you no longer need. You “purge” the model either via the Model Info statistics tab or an extension to get rid of the Definitions you no longer need.
There is some slight-of-hand involved in some of the manipulations of Components.
For example, you create a new Component by selecting some collection of items in the model and invoking “Create Component” via your favorite choice of menu, right-click menu, keyboard shortcut, etc. What actually happens then is that a new Component Definition is added, capturing the general structure of what you selected, and a new Component Instance is placed where the selection was. You have the option to skip the creation of a new Instance by unchecking the “replace selection with component” box in the Create Component dialog, in which case you get a new Definition but the original items remain loose in the model. This can happen by default if there are unselected items touching the ones you selected. Forgetting to check this box is a frequent source of confusion to newbies.
When you open a Component for edit, you are actually accessing the Definition via a selected Instance and editing the Definition. That’s why the changes immediately propagate to all the other Instances of that Definition.
Now finally to your question
I don’t see how that would create nesting. “Nesting” means that a Component Definition (the “parent”) contains one or more Instances of other Component Definitions.
When you invoke “make unique”, a new copy of the Component Definition is created and the selected instances are re-tied to that new Definition instead of the original one. You may note that make unique isn’t available unless everything in the selection is an Instance of the same Component.
There is no reason why make unique would create nesting.
I don’t see an issue with the method you describe.