The cooling performance between the two is minimal (2-5C) on a 95W TDP CPU for example. I have the Dark Rock Pro 3 and it performs very well and is very quiet. The difference is that with the Pro 3 you have much higher thermal headroom (the heatsink can hold much more heat before it saturates). This is useful if you do CPU computational tasks over long periods of time (like I sometimes do). So pick the one that best suits your needs and space. You also won't see the RAM (you also need low profile RAM) with the PRO 3 version.
Also I think the price difference between the two is minimal so that is why I went with the better performing Dark Rock Pro 3.
P.S. I installed it outside the case on the motherboard and then put the whole thing...