The shadows were done with a script.
GIFs should work with camo the same as PNGs. There was a change to allow colors within the unit icons (there are some icons now that express this, but this work can't be done by a script, so it's much slower going than the shadows). Any pixel within a icon icon that has different values across the color channels will be considered a color, and ignored for purposes of camo. So, it might be possible that the pixels in your GIF that you want to be camoed, don't have the proper pixel value.
One difference between PNGs and GIFs is that PNGs support an alpha channel for transparency, so you don't have a specify one "transparent" color like you do with GIFs.