Until today i was using the Flash IDE to add compression to .png files, then exporting them inside a .swc file for use in FDT. No need! The embed tag has a compression parameter.
public class Main extends Sprite
{
[Embed(source="../assets/star.png", mimeType="image/png", compression=true, quality=90)]
private var Star : Class;
public function Main()
{
var star : Bitmap = new Star();
addChild(star);
}
}