I would say we should make two entries for the 3DS and PS4 version like what we recently did with Farenheit for the Sega CD / CD 32X. Designate the different versions in the cart/disc/media section in case you have one but not the other, but if you have both you can add both entries to your collection.
That's probably the best we can do I would think, because we can't ascribe the game to only one platform by default since it comes with two of them. We can designate that it came with the other version in the description