The differance is that Dark Matter came about because scientists made an observation that the behaviour of the galaxy didn't fit our current understanding, the edge of the galaxy spins to fast considering the amount observable matter. Therefore they hypothesised that there is more matter that we can't see directly.
Now I can understand the argument you can make is how's that different from the "watch maker" arguement, however we have other theories and hypothesis of how many of these "complexities" can occur naturally with out a creator, and on top of that having a creator isn't that much different from having the universe occur spontaneously (at my level of understanding anyhow, I realise that there is more to this but I can't competantly use it to support my claims) as at the end of the day day it doesn't give a true beginning, where did the creator come from?
So up to here I'll give them a level standing for the sake of argument. However this is the important bit, scientists are testing various hypothesis to explain dark matter, for example:
http://xenon.astro.columbia.edu/ testing for WIMPs weakly interacting massive particles
http://icecube.wisc.edu/ testing for neutinos
also a relatively new idea, currently we don't have the technology to carry it out but if/when we do the results could be interesting, this is observing the behaviour of Eris and its moon to see if quantum fluctuations can explain dark matter:
http://www.newscientist.com/article/mg21729014.500-dwarf-planet-eris-may-reveal-quantum-gravity.html
How ever as far as I'm aware no one has carried out a credible experiment that has been replicated to test for a creator.