According to this discussion, the only codecs that WinRT apps can use either must be supplied by Microsoft or bundled into the app. WinRT apps cannot use any codecs installed from the desktop, and there doesn't appear to be any way to make a 3rd party codec available to all WinRT apps.
This behavior is by design. In order for you to use your FLAC MF codec from within the context of your Windows store app you will need to modify the codec to work in the WinRT environment. You will then need to ship the codec with your application rather than rely on a desktop installation.
Edit: More information from @Bala Sivakumar, Program Manager for the Microsoft MM Platform Team
The reason for this is that Windows 8 is designed to run on low-power devices where software decoding is not desirable. Therefore only codecs that can be hardware accelerated are supported system-wide. Third party codecs can be made available in some cases - where the graphics card manufacturer supports hardware acceleration of the codec and ships support in the driver. Such codecs are signed by Microsoft to allow for system-wide use.