Sorry, no, Aperture is not a compositing application. If you want this sort of functionality for still images, Photoshop's basically the only game in town. You could do similar things with alternatives such as GIMP or Pixelmator, but if you're serious about compositing, you need an compositor that supports more than 8 bits per channel, and AFAIK Photoshop is the only 2D image editor for the Mac that supports this.
Aperture does support such images, but lacks layering and abilities to isolate color channels that you'd need for keying/mattes.
If you want to do this for video, however, Final Cut and Motion do have Chroma Keying abilities.