You can also look at using the other GIF animation techniques, which uses the same virtual canvas and canvas offsets methods (just no complex disposal methods). http://www.imagemagick.org/Usage/anim_basics/#coalesce
Especially look at the 'gif_anim_montage' script. which 'dims' previously overlayed images, so you can see how th new image overlays and what parts it draws, relative to the other overlays.
yes this is all commandline, but it should all be directly translatable to MagickWand programming.
If you are just wanting the final image use Flatten (with the approriate background color. http://www.imagemagick.org/Usage/mosaics/#flatten
If the individual layer are smaller. -trim will trim the edges and retain the canavs and offset information as appropriate. To remove the colors in overlays that don't chnage the results use the Transparency Optimization methodhttp://www.imagemagick.org/Usage/anim_opt/#opt_trans
It replaces any overlaid pixels that don't change the background (more than the current -fuzz setting) with transparency.