Nitrogen takes a lot of shortcuts. It's not nearly as complex as the built-in tool. This has both plusses and minuses. Terrain generally isn't as smooth as stock RWG, though stock does have some areas that are pretty rough as well. You can customize the map a lot more with Nitrogen, especially in regards to POI and biome layout, but it's more likely to have placement bugs than the stock mixer.
Also keep in mind that Nitrogen has not been updated for a19.0 stable, much less up to a19.3. As a result, the process it's using is a few versions behind the default RWG mixer, and this creates some major compatibility issues. Right now it's basically "use at your own risk" tool, that may cause game-breaking bugs, and may not ever be updated again.
The community is pretty handy though, and if you've got questions or issues, they are very open to assisting.