An article is its own Content Type and has its own Tags. A Discussion thread is its own Content Type and has its own Tags. When a discussion thread is associated with another content type (Resource, Showcase Item, Articles etc), the TAGS don't MAGICALLY become one in the same. The Content itself gets tagged through that Contents Tags Handler. Same with the Discussion thread.
The TOP ROW of tags below to the ARTICLE. They are managed by the Article.
The Bottom ROW of tags belong to the Discussion Thread. They are managed by the Discussion thread.
They may LOOK like they are duplicates, but they are actually 2 sets of Tags for 2 different content types (Article Tags and Thread Tags). They just happen to be the same tags. If you EDIT the Thread and remove the thread tags, the Article Tags will not be effected as they belong to the Article.
The XFRM decided NOT to display the RESOURCE Tags in the Header of the Discussion thread because it was causing confusion. I have (TODAY) REMOVED the Articles Tags from being included with the Article Header on an associated discussion thread. The REST of the Article Header data will continue to display (Title, Byline, Custom Fields, Attachments, Social Sharing buttons).
As of AMS 1.3.8, Article Tags will NOT display in the HEADER of an Associated Discussion thread.