1. This question I will have follow up for you but I believe we use PhantomJs to make make the page calls. This is essentially a headless version of Chrome. As I say I will check this answer for you.
2. The length of time is determined by the amount of url's in sitemap.XML. But overall the process does not take very long. Site Scan is unable to access pages that are behind a login page. This were you would need to use our Chrome Extension and continue the process manually.
3. No, is the simple answer. Site Scan has no knowledge of additional pages linked in anchor tags. As I mentioned above these could be added through the Chrome extension.
If you have any further questions please contact your account manager who will be happy to help.