From my personal understanding, all OS Api provided by Windows NT Platform are implemented throught C/C++ headers files, which means a non-C/C++ programming language has no way to directly access these Api-s.
On the lowest level, Native API are provided for programs who intend to interact with the OS before any non-booting windows components have been loaded, such as kernel32.dll (who implements the WIndows API). The question regrarding whether Native API can provide overlapping functionalities as opposed to Windows API is not clear for me. However, an article in technet/Microsoft Social pages described Windows API as "higher level" API compared to Native API,see reference 1, this implies that the implementation of Windows API is at least partial wrapping of the Native API. These API-s have few documentations available. A read on the source files might be one approach to reveal the API details. Details regarding how to access these API-s is still not clear unless a thorough research is conducted.
Windows API, informally WinAPI, is the core set of application programming interface provided by MS operating system family. The name "Windows API" collectively refers to a number of different api implementations on different platform. For specific, on a 32-bit windows OS (Win XP, Win 7etc), Win32 API is the "Windows API"; on windows 8, both WinRT API and Win32 API are the "Windows API" for desktop and windows shop application respectively. It is worth to note that the Windows API for a 64-bit Windows OS is still named Win32 API, although the API implementation is 64-bit customized. All Windows API are provided through a header file called Windows.h, in which a number of child header files are included,see reference 2. It is worth noting that Win32 API is implemented through C Language, and is therefore implemented in a manner without any object oriented feature.Can be introduced by inlcuding "windows.h" file.
The Microsoft Foundation Class Library (MFC) is library that wraps portions of the Windows API in C++ classes. Through MFC, Windows API can be utilized by calling member functions of the objects created from MFC classes. MFC can be accessed through a header file called afx.h, in which a MFC base class named CObject is defined to expose MFC Classes as the application interface. Not all classes in MFC library are included in afx.h.
Reference Table:
http://social.technet.microsoft.com/wiki/contents/articles/11831.the-windows-native-api.aspx
http://en.wikipedia.org/wiki/Windows.h