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Hi Noemata,
This issue does not seem to be specific to IoT. I recommend you look to the larger Windows 10 forums for a discussion of FLAC on various Versions of Windows 10. See http://answers.microsoft.com/en-us/windows/forum/apps_windows_10-groove/flac-media-player-in-windows-10/0f6f0f87-d535-450c-bdfd-3e57ebb4124d?auth=1
NOTE: If you are a member of Windows Insiders, that would be the most direct way to give the OS team feedback across multiple Windows 10 platforms.
Sincerely,
IoTGirl