As both Qt and MFC are wrappers around the native OS functions for managing windows and other OS utilities (that use Win32 API under the hood and look completely native) there is really no reason to consider the use of MFC over Qt, as it is not more native than Qt. Either your definition of "native" is broken or you haven't told us the whole story.
But there are a thousand reasons for considering Qt over MFC, as the latter is a complete pain to use, whereas the former is a cleanly designed, easy to use and still highly flexible library (that strives for nativity by any means possible).
The only way you might see MFC as more native is that it comes from Microsoft (the same company that developed Windows). But that doesn't make it more native. It's still a third party library. This third party worked for the same company as the party developing the Win32 API, but that doesn't make it specifically more tied to the Win32 API, as both were developed independently (and surely by different people).
Do Qt apps look and feel native under Windows?