In a scientific paper, the author would just write down what they do, and trust the reader to be experienced enough to discount such problems themselves. Now, journalists write for a general audience, that is they write for the lowest common denominator, and accordingly the question what they should write there becomes a quite interesting question.

So, 538 did actually change their error estimate during the 2016 campaign to better account for problems of correlation. From a purely mathematical standpoint that is kinda the wrong thing to do, but it is arguably better in line with what the readers expect an error estimate to be.