As someone who is only now making the transition from Python 2 to Python 3, losing the numbering in the documentation on the Python Standard Library slows down my navigation when looking through the high-level contents.  

Given that the position of sections hasn't drifted much between versions, being able to treat the sections like chapters of a book affords faster access when I can quickly identify my position in the page without having to look at the scrollbar, provided my operating system even displays one when I am not actively scrolling.  Knowing that there are roughly 40 top-level sections in the library means I can find something I know to be in the middle much more quickly from its number (plus or minus version drift) and those of its local surroundings than by its overall position in the page.  Moreover, losing this feature can only be mitigated by search or "find in page" provided I remember modules and their contents by name, correctly spelled.

I appreciate the overall cleaner appearance as sections become heavily nested that is addressed by this enhancement.  I do however respectfully disagree with the choice of doing this at the expense of top level ordering.