The family table would still be within the 1 assembly. Each entry could be your Assy # and would specify if the parts is included in each assy level in the table. The family tables would only serve the purpose of building and managing this table, or you can use them for additional drawing views by adding the family table instance to your drawing.
There may be other ways I am overlooking. Again, tables are not my strong suit. I tend to build them manually for full control.