They take polls as given.
Polls-plus is simply polls + weighted adjustments based on state by state demographics, endorsements, and national polls.
If all the polls are wrong, there is a systemic issue with how the polling was conducted, likely due to how the polling companies evaluated a 'Likely Voter' in MI.
The only way to know that the polls were wrong in this instance (that this issue existed) is through results.
MI hasn't had a real primary in 24 years. There was no historical data to draw from for this state, which is probably where the fault in polling came from.
538 aren't magicians or soothesayers, they analyze data with an additional layer (or two, or three, or four layers) of data to make an analysis. If ALL AVAILABLE DATA points to a 20 point victory, there will likely be a 20 point victory.
Nate mentioned in one of the chats that he had a hunch that MI was going to produce some wonky results (likely he saw the gap in historical data in addition to some significant gaffs in polling MI and wondered if the polls could be using a faulty method), but there was no data to support it (which is why he also mentioned you should ignore his hunch).
So basically, MI had a polling error that was pretty bad. Now, we can pretty much ignore the MI polls and look at the results.
What data can we glean from the results?
Sanders seems to be doing better with black people in the north: 6.5/3.5 split with Hillary, as opposed to 9/1 in the South. This particular point should already be evident in polls of northern states, but there really aren't many available as of now (courtesy of a south-heavy beginning of the election cycle).
Sanders does better in open primaries by a significant margin, and has a lot of cross-party support as compared to Clinton (especially in independents). This particular point may be the most salient in looking at future polls, as it will throw off the Likely Voter formulas in most polling agencies.
So if you want to take away a point, look for open primaries still on the calendar, look at how polls for those states identify likely voters, look at registration numbers for independent voters in those states, and (based on comparable data in MI) adjust the forecast.