I've been cleaning the book archetype's makefile this afternoon. I suspect there is no list of chapters because the example is quite minimal. Enterprise Pharo was the one Thibault and Yann worked with, so I need to compare with it.
The recent work on pillar was about removing superfluous responsabilities and moving it towards a simpler markup renderer. Chapter numbering is a global information, which is OK in LaTeX because it can be computed by TeX during its compilation pass; however HTML chapters are just generated one for one following the pillar files.