Branching order in a tree is directly related to taxonomy, while branch lengths have more to do with evolution. For large-scale phylogenetic study across many phyla the former is more important than the calibration of branch lengths. The latter is based on the assumption that mutation rate is more or less constant. This assumption cannot hold when dealing with many phyla.
Part 3.1 The figure legends require more rigorous explanation. Would be interesting to remember that the branch lengths are not taken into account, or were omitted.