Can it it in a Bitfenix Prodigy - absolutely, you have all the room in the world.
Is there a suitable motherboard to support it? Doesn't look the case. - EDIT - It seems like the ASRock Z87E-ITX does fit this cooler, though it's obviously the wrong socket for you. It would also have a pretty huge overhang which may fit in a Prodigy but will cause issues in most cases.
The NH-D14 fits on your board, but it doesn't leave much space, and it would appear that even though the NH-D15 is only 10mm wider overall, it is a step too far. Quote from Noctuas website -
Due to the VRM-heatsink the cooler can only be installed in 90° orientation. Thus the memory modules mustn't be taller than 31.5mm.
I'd have guessed if anything, it would have come into contact with the graphics card area, but this would suggest that actually, the upright daughter-board is the issue in this case. As a 90degree rotation makes no sense here, I think it's safe to say it's a non-starter.
Tbh, it's likely your 212 is probably good enough for what you are doing, unless you are really desperate to push your CPU further. An NH-D14 or Phanteks PH-TC14 should fit, along with a graphics card, but depending on the rest of your components they may require the removal of your rear exhaust (they will effectively self-exhaust as they line up pretty well with this area anyway).