ACM and Media Foundation Transforms are two completely different things. You can have a codec as ACM but not MFT and the other way around. So just because you have an ACM MP3 encoder, doesn't mean you can encode MP3 with Media Foundation.
You can use the NAudioWpfDemo application that comes with the NAudio source to explore what Media Foundation Transforms are installed on your computer.
And no, there currently isn't support for creating a MediaFoundationReader from a stream.