It would help if the problem was due to bugs in the actual MF playback, but the major issue in most cases is the codecs used. If they're using any of Microsoft's codecs, it's never going to work with stock Proton until Valve's transcoded duplicate videos are downloaded for the game.
This isn't a problem. Proton hooks the video data as it's being played, it doesn't matter where or how the files are stored.
I think the code is here:
Proton/media-converter at proton_6.3 · ValveSoftware/Proton
That's the client side anyway. It saves the data being played to disk which is then uploaded to Valve by Steam any time there is a cache miss (meaning the video fails to play and the user sees a test pattern).