The content plugins, in Joomla and K2 in general, are triggered on the 'content' of the article. They can only manipulate the actual article text, not extra things like the "This Author Articles" or the "Author Box". Those aren't part of the article contents itself, they're actually part of the template you're using and are 'outside' of the content.
So, when a content plugin is triggered, we can only prepend or append to the actual content that is handed to our plugin, which doesn't include any of those things you're looking for. There's not a way around that with the content plugins. The only way to force the comment box to be below the other sections would be to actually embed the {JFBCComments} tag in the K2 template itself underneath where the author box/links render.
Hope that at least explains the issue, but we'll agree, on some sites, the positioning isn't always ideal.
If you need anything else or have other questions, just let me know,
Alex