Under Wine (when using a winegstreamer source), we don't use an MFT to decode, that is done by the media source.
This is pretty much the problem, and it needs to be changed. This is what winedmo does already and I have no objection to make the winegstreamer media source do the same.
The MF pipelines should be working well now as they are used for most of the MF media playback, assuming we pull any remaining Proton patches in the MF modules (which I don't think are many left).