Are you aware of this bug, that the Contour component is creating duplicate curves?
Aside from that, it would be easier to answer your question if you posted your code with internalized geometry. Other than the bug, I believe Contour produces the data tree you want.
P.S. If you must use your contour lines (from a scan?), there is a way to create the tree you want using MIndex (Member Index). It is a variation of this model: