@wonkyum lee I've been able to create fragmented mp4 files with MediaCapture by changing the container subtype. Perhaps you can do the same with MediaTranscoder. Try something like this:
// taken from C:\Program Files (x86)\Windows Kits\10\Include\10.0.17763.0\um\Mfidl.idl
static readonly Guid MFTranscodeContainerType_MPEG4 = new Guid("DC6CD05D-B9D0-40ef-BD35-FA622C1AB28A");
static readonly Guid MFTranscodeContainerType_FMPEG4 = new Guid("9ba876f1-419f-4b77-a1e0-35959d9d4004");
with
var encodingProfile = MediaEncodingProfile.CreateMp4(VideoEncodingQuality.HD1080p);
encodingProfile.Container.Subtype = MFTranscodeContainerType_FMPEG4.ToString("D");
Hope that works for you!