I think what you are referring to is the "Live Links" feature in AMR. I don't think Magic Submitter can extract those unfortunately. Possibly If you create your own template.
You can't do this. MS can't find published article links.
You can get the live links from the link manager. The problem is that MS won't give you the links until you submit another article under the same account. For bookmarks and such its instant but for articles which may take time to be approved it checks each time you submit under the same author account. Really its a good system when you get used to it.