More, rather than less, capitalisation is becoming the norm; usage is making the incorrect normal and, thus, correct.
In the first example, I assume that the author is copying the style of the title/heading to that section which will be "Chapter Six", this is justifiable rather than correct (unless placed in quotation marks, when it would be correct.)
In the second, the author is using capitalisation correctly.
At the moment, I think the version with capitalisation prevails, at least in academic contexts. At present (who knows what I might do in the future), I would write, in an academic context, 'in Volume 2, Section 9, Chapter 3, Book 6' (assuming that the section constitutes a large segment), but 'in paragraph 3, stanza 4, on page 7, line 12'. In other words, capitalisation for larger segments. Therefore, no capitalisation for chapters in the books of the Bible.