It sounds like he's just been hearing from people who were interviewed by Mueller.
The headline is trying to make this sound like more than it is, but if you read the article, the writer is using Trump's morning tweets to make all sorts of leaps. There are three options presented for why Trump "knows" the inner workings:
People who have been interviewed by Mueller are telling him about it. Or he's reading accounts in the media (not like Roger Stone has been quiet about things.)
Trump has been interviewed and is speaking from his first-hand knowledge.
Whitaker told him inside information.
Of these three, the first is by far the most likely.