As a method CVTree is independent of 16S rRNA analysis. First, it uses protein products in a genome instead of RNA segments in the genome. Second, it does not do sequence alignment. CVTree generates stable trees but cannot tell which branch corresponds to what taxon. Only after comparison with the existing classification and nomenclature one would be able to make connections with taxonomy. In this sense it does depend on 16S rRNA taxonomy. Anyway, CVTree does not challenge 16S rRNA analysis but makes it more convincing in most cases. The revealed discrepancies call for further study.
Conclusion I disagree that CVTree approach is independent of 16S, because authors are using the current accepted classification (which is mainly 16S-based) to validate the observed clades.