Looks like a lot of transitioning towards ePub 3 while leaving the existing ePub 2 features in place for maximum backward compatibility.
You don't have to change the way you do covers, the old way will work fine (method 2). Method 1 is based on an ePub3 OPF file.
That's the NCX file in ePub2. Nothing has changed there as far as I can see. And an EPUB Navigation Document in ePub 3. The Navigation Document has the advantage of being a Logical ToC and an HTML ToC all in one.
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I don't understand 3.4 "landmarks nav Elements Guidelines" at all. What are they for? Do you have to use them?
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Landmark nav elements (ePub 3) are similar to the guide items in an ePub 2 NCX file.
It looks to me like Kindlegen v2.8 is accepting ePub3 as input (or at least XHTML with an ePub 3 OPF), but you're obviously not required to do so.