It was never really in doubt that Logan would be an R, especially given how its trailers have shown a level of gore that wouldn’t fly in a PG-13 movie.
Think Jackman’s own brief appearance in the nude in X-Men: Days of Future Past, for example.
The biggest bit of new information here is the mention of “brief nudity”.
Of course, knowing what is needed for certain ratings is a core part of the filmmaking process, with most blockbusters treating the PG-13 guidelines (it’s the most lucrative classification) like a checklist.