Blown out of all proportion.
I remember a few months back from the original article, it was only one make/model of HSF that damaged a Skylake chip, one occurrence. Turns out the HSF didn't follow Intel's specifications for the amount of weight/pressure of the mounting mechanism.
I've had a NH-U12S fitted to my 6700k for almost 6 months with no issue. I also setup a similar system for a friend with a NH-D15 again with no issue, he's even driven the system 300 miles on the beak seat of a car.
The only implication of a thinner CPU substrate is the increased difficulty of delidding them using traditional methods. This is no longer an issue since the 'delid' tool takes take of that flawlessly, for those inclined to do so.