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My Xpath knowledge is poor but can you find a way to construct an expression which combines your level1 toc Xpath and level2 toc Xpath in an either/or Xpath expression and put it in the --chapter setting.
Alternatively, you could cheat! Create the epub with all the correct TOC entries at a single level, then edit the .ncx file (either manually or using a utility like Nigol's epubfixer utility) to nest the entries correctly and/or remove any unwanted entries.
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