I'm no sort of expert on it, but it seems to me dark matter is a little bit like the hypothesized mystery planet that was once thought to explain the anomalous orbit of mercury*.
Ultimately it turned out, of course, that the odd behavior of Mercury was due to the differences between Einsteinian dynamics and the Newtonian model. And the issue existed because the Newtonian view didn't quite match reality, rather than because there was an extra, unseen, planet between the Sun and Mercury.
Interesting that at the other end of the Solar System it worked out differently - the odd behaviour of Uranus was because there _was_ another physical body out there, i.e. Neptune. So seems that sometimes there really is another entity we haven't seen, and sometimes it's that the theory is wrong.
Likewise, perhaps Dark Matter actually exists, or perhaps it's an artifact of incomplete theories about gravity?
I don't see that "God" really fits into this either way.
* I gather it was provisionally called "Vulcan"