You can use groups for walls too. It used to be a problem with groups but not anymore (I personally prefer components).
It is preferable to have the walls windows and doors all in the same nesting level like here:
flextools structure in outliner 01.png
You can change the name of the door (definition name) and everything should be fine.
The numbering sequences in component definition names are how Sketchup and dynamic components work. When you make a copy of a dynamic component it keeps the same name, but once you make a change to one of the copies it becomes automatically unique and Sketchup appends a #n to the end.
I am not sure what happened in your example but the wall cutting can break when changing the context of a wall cutter in outliner. See here examples how to avoid breaking the wall cutting: https://flextools.cc/learn/wall-cutter/#Advanced-Operations
Mike Brightman just came out with a new system in ConDoc 5 for applying multiple SketchUp tags to one object. I haven't tried it yet, but I believe it will free you up from worrying about component and group nesting levels giving tools for easier filtering and sorting.