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Within the constraints of having everything in one case, though, a watercooled system means you can have more / bigger fans cooling more / bigger radiators, by dint of not being restricted to being stuck to the cpu / gpu.
But yes - having the rads somewhere different entirely would be better. As would cooling with freon.
The point is, if you're going to move your radiator away from your CPU, which is what water-cooling hoses allow you to do (as @useless says above, a conventional CPU cooler still has heatpipes and a radiator, they are just close to the CPU), it does not make sense to position it or its fans so that its heat is dumped into the case rather than out.