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I can't answer the first one (I never read the guide), but I can the second. Those are two different TOC's. In ePUB2 there must be an NCX file, which is used at TOC. Without it, the ePUB2 is not valid. The NCX can be generated/updated with the second option. That is also the TOC you can see on the right panel of your screen (usually). Your reading application or reader must support the NCX and uses that to display the TOC.
In ePUB3 the NCX is deprecated, but allowed for backwards compatibility. Version 3 of ePUB uses a XHTML file for the TOC. That is the other one. For an ePUB2 it has no real added value, although some publishers and editors will still put it in anyway. Some find it pleasant to have a real TOC as well as the NCX version. It can have some uses.
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