ALL 2016 MKXs can be flat towed. But you can't get a baseplate for one with Adapative Cruise Control. Other than that restriction. ALL 2016 MKXs can be flat towed.
Here's what happened - when the 2016 first came out they had a software issue where they would not go into Neutral Tow mode. Lincoln did two things. First they told all dealers that the cars could not be flat towed THEN they fixed the software issue on all newer cars (and they retroactively upgraded the software on those 2016's with the problematic software).
It seems the dealers only registered the first "do not tow" info because they didn't want to be stuck returning vehicles.
It's in the current manual. There are no retractions about this feature. Lincoln will confirm this. If you happened to get an older 2016 that won't go into Neutral Tow mode all you need is a software update. All others - that will go into Neutral Tow mode are good to flat-tow. Just like the manual and Lincoln says.