So the user doesn't know if its either a new article, comment, etc.
The red number (called 'counter') on the Articles Navigation Tab = the count of Unread Articles. There is no indicator of unread article comments.
Kind of like the same behavior with unread forums?
If you are referring to the Forums TAB itself, Core XenForo does not use the ['counter'] element for any of the core Navigation Tabs. The Forums navigation tab does NOT have an unread Threads indicator, nor is there any code that makes Forum Tab sub navigation elements BOLD.
With that said, there is 1 core XF addon that does make use of the 'counter' for its Navigation Tab. XenForo Media Gallery has read marking for both Media and Comments, however, the unread count on the media tab is only for Unread Media (not comments). Here you can see that the media tab is showing 1 (as in 1 unread media item).
As you can see, XenForo Media Gallery does not have a BOLD indicator anywhere in the dropdown version of the sub nav for the Media Tab just like the Articles Tab for AMS, so once again, there is no "just like xenforo does it" involved here.
The indicator on the Media Tab is for the count of unread (unviewed) Media Items.
When I view it, the indicator disappears because there are no more Unread (unviewed) Media Items. However, lets click on the new media comments..
As you can clearly see, there are 2 Unread Media Comments, yet, the media tab does not display a red 2 as the indicator for the tab is only associated with Media Items, not comments.
So as you can see, AMS is behaving the same as XenForo Media Gallery for its usage of the "Unread" indicator ('counter') on the Navigation Tab.
XenForo Resource Manager does not have any code that tracks whether resource content is Read or Unread, so it does not even have a listener to add a 'counter' to its navigation tab.
If you see a site with unread threads indicator on the Forums tab, its being done by a 3rd party addon, not Core XF.