It's not two different opinions, as our opinions are basically the same (file the top of the nut right down), but our preferences are slightly different (I am quite a pedantic person ).

Technically it's all about minimising the risk of a bit breaking off the nut and making the guitar unplayable.

I normally use a set of strings for setting up a guitar and then replace them once that's done, so it's easy enough to arrange that the last thing I do before swapping them is to file down the nut until I'm just catching the top of the set-up strings, then remove them to sand smooth and polish the nut before fitting the new strings.