Unfortunately that’s unlikely to happen for two reasons:
- The homepage is generally speaking the most visited page of a website. It would always appear at the top of the list, and to the visitor -who likely already knows how to go to the homepage- it wouldn’t make much sense to always see it under a “Popular” list.
- Tracking visits is usually resource intensive. Being the homepage the most visited page of a site -as stated above- would likely affect your site’s performance significantly: aside from posts and pages, the plugin would also need to track views to the most visited page of your website.
So, while it might sound like a good idea, the reality is that for the vast majority of sites out there using the plugin it wouldn’t really bring any significant benefits.
If all pages are tracked it is more easy to tell if visitors click on certain content when entering the frontpage or just exit.
WordPress Popular Posts doesn’t provide such statistics. It seems to me that you’re thinking of Google Analytics (which btw can already tell you when exactly are visitors leaving your website if that’s what you’re interested in).