I fit a Noctua NH-U12P in my parent's Prodigy. Lot's of room to fit and didn't need to mod anything. The newer NH-U12S is no bigger than the NH-U12P that I used so you should have no problem fitting it.
I need help with this too... You see, the Asrock Z87E-ITX's CPU socket is placed too ridiculously far from the pci-e slot as compared to Asus boards which have their sockets just nice in the middle. Will this Asrock motherboard fit the prodigy with the NH-U12S fine without any real problems like the heatsink touching the side panels whatsoever? Thanks.