yes exactly that's exactly why its better.
it is better because you can use a better, bigger, thicker rad, with better, quieter fans, with a better water block, with a better pump. The h100i uses the lowest end parts to achieve its task.
in terms of warranty, yes you are right, nothing can beat that. however, In a custom loop, the only thing that can really fail is the pump, which takes a while if you buy a good once. (this is aside from leaks caused by improper installation)