Each piece is made from fondant (which I highly suggest Duff Goldman's fondant found at Michaels, it actually tastes good and is easy to work with) and done in steps. In the photo above, each piece is made one at a time, but if you look at how it's constructed, there's no reason you couldn't cut out the bones of each piece all at the same time.
Try busting out a pizza cutter to make all of the "crusts" and use a large knife or bench scraper to cut all of your pie pieces in a few quick strokes. The whipped topping is just a long snake, why not roll it all out and cut it into small sections? I'm willing to bet you could assemble a topper for each cupcake in less than a minute once your pieces are cut and when it comes right down to it, that's only the time it takes to watch a tv show (assuming you're making cupcakes for 50!), because we're all about multi-tasking!
(Image: Cake Central)