Yes, 16S rRNA phylogeny is quite stable and it almost defines the present taxonomy. We have given due credit for this. In general, CVTree does not challenge 16S rRNA analysis but complement it.
Archaeal phylogeny has already been studied in detail, with 16S and other marker genes, and with genomic approaches too. Some of the undersigning authors had already published on this before, although with smaller input datasets. Therefore, the fact that 16S topology is quite stable and comparable with other approaches is already known.