This looks intentional as Media Foundation API suggests that you let the API choose appropriate encoder for you. Your role there is to build a suitable profile and let transcoding API to create the topology using requested parameters.
I suppose you know the MSDN leads, but for the record: Tutorial: Encoding an MP4 File - Create the Transcode Profile.
In particular, they seem to want to retain control over encoder choice in order to use hardware encoder automatically where applicable:
If a certified hardware encoder is present, it will generally be used instead of the inbox system encoder for Media Foundation related scenarios.
One of the problems with compressors in DirectShow was the common list and competition between compressors. For many reasons, an application would rather hardcode specific compressor rather than use the best choice for given format. Here in MF the approach is different: a profile defines what you want to eventually get on the output, then API takes responsibility to supply the encoder.