Rankings are fundamentally different from ratings. And each ranking system does its own thing.
Who has performed best in a particular limited set of recent events? Look at the ranking.
Who is the most skilled based on all the data available, without weighting specific recent events? Ask a ranking system.
The WPA and WNT rankings use different points systems and mostly different events. The one with the larger participation by the top players will give more "reasonable" rankings, if it uses a good -- or at least not too bad -- points system.