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There is the IMFPluginControl API which looks like exactly what is needed.
Unfortunately, it doesn't seem to apply to the Source Reader or Sink Writer or CaptureEngine or MediaCapture APIs. They will continue using transforms that have been disabled using IMFPluginControl::SetDisabled.
For me, this seems like a bug since exactly in these cases this functionality would be useful, since there is no other possibility to control which transforms are (not) used (if there is, please let me know).