To keep the alpha channel, you should convert your source (e.g. a playlist) object to ARGB32 format with:
vidProps.fccType = eMFCC.eMFCC_ARGB32;
m_objPlaylist.FormatVideoSet(eMFormatType.eMFT_Convert, ref vidProps);
To get a PNG file, you should get an item of a playlist and grab a frame from it. Like this:
MFrame frame;
MItem item;
string path;
double offset;
m_objPlaylist.PlaylistGetByIndex(-1, out offset, out path, out item);
item.FileFrameGet(0, 0, out frame);
frame.FrameVideoSaveToFile(@"d:\testPNGfromTGA.png");
If you need the current frame, you should use ObjectFrameGet method instead.
To export video with alpha layer, you can use these codecs:
format='mov' video::codec='png'
format='mov' video::codec='qtrle'
Please note, that these codecs will require more performance usage.
If you want to change the background of the video with the Chroma Key feature, you need also set a transparent background of the mixer.