It seems like this is basically just the same thing that Mono has done for a long time with AOT. I'm not really sure how it differs from the Ngen tool, though.
The biggest difference with NGen is the fact that .NET Native doesn't ever "fall back" to JIT compiled code. There are other differences--refactored runtime, static-optimized libraries, static marshalling, etc.--which can be seen by the perf wins over NGen. We're seeing 40% startup performance gain over NGen apps for top Windows Store apps.