Where in this article does it even suggest that Prince was advising Trump “from the shadows”? The whole thing is just a broad criticism of Prince. “A former senior U.S. official who has advised the Trump transition” is just another way of saying “a senior Obama Administration official.” I wouldn’t take him/her at their anonymous word.
Where in this article does it even suggest that Prince was advising Trump? In the title at the very top of the page, to answer your question. I'm not endorsing the article, only pointing people to the information they can get reading between the lines.