WBUR, Boston's NPR news station, published in their blog "Cognoscenti" an article titled "Why Donald Trump will Win in November" in May of 2016 (https://www.wbur.org/cognoscenti/2016/05/06/election2016-tru...). I can't think of anything more representative of what people think of as the left leaning intellectual class than a Boston NPR blog with a Latin title.
This idea that him winning in 2016 was inconceivable to media/intellectual circles is a bit of revisionist history.
A single contrarian take doesn't undermine that trend.
The mainstream media and the intellectual class have very little overlap.
What there was, was a diversity of opinion and vigorous debate (sometimes devolving into sniping, sure), the thing that is supposed to be there. There wasn't a 50/50 split, but I don't remember a single publication I read at the time (all the classic left leaning intellectual rags) that didn't run pieces predicting a Trump victory.
That prediction was correct, and by a decently large margin. But losers often become president because of the electoral college (it's happened 5 times already), and losers will continue to benefit for years to come.
A number of people in the intellectual world did, or at least wrote articles purporting to explain why it was more than remotely possible.
The relatively new set of people in the major media trying to play the poll-based mathematical prediction game that Nate Silver started with 538 who weren't Nate Silver undersold the chances of it happening because they made the naive mistake assuming that deviations from polling averages between states were independent of each other rather than, as historical analysis of the type Silver does would show, tightly correlated. But “media outlets want what Silver does but can't afford to pay to have Silver, or anyone with anything like his level of skill at what he does” doesn't represent the “intellectual class”.
I'm not sure even Jill Stein or Gary Johnson would really be a black swan event, given that I can list it as a possibility, but it's definitely a lot more gray than "either the Democrat or Republican wins".
There is no need to explain where an "enormous hidden body" of votes came from because it didn't. There is no need to explain why the polls were wrong, because they were as accurate as they normally are. There is no need to explain why elites were wrong about what the people thought because they weren't. And there's no reason to argue about whether the election was rigged, because Trump said it was.
Political intellectuals tend to lean left, and whenever a rightist scores a major political victory they start predicting stormtroopers goosestepping through American streets Real Soon Now, going back to at least Reagan. So the Nazi Revival is generally accepted as real, and if you contest the idea's truth you may be considered one of them.