1. Creating a symbol from a layer containing existing symbols keeps the existing symbols linked to other instances outside of that layer. The problem is if you later want to detach the super-symbol, all of the contained symbols are also detached. I think the simple solution is to just detach the super-symbol / skip over children that are symbols themselves.
2. (See Attachment) What if I have a bunch of symbol instances in a pattern and want to duplicate the pattern and make alterations to the symbol instances while keeping the changes separate from the original pattern, i.e. duplicating the symbol & pattern together? I couldn't think of a good way to accomplish that.