As a scientist, am I discovering how God rules his universe, or am I determining the behavior of this object which is inanimate and has no reference point outside itself? Both answers permit me to use the scientific method (indeed,the philosophical substrate of Xty launched modern science itself), but the assumptions I draw about the nature of the universe I am in are vastly different.
That is the problem I have with Dawkins. Both "starting" points are equally valid in science proper. There is NO intrinsic reason why an empirical basis should be the starting point for scientific endeavor, much less the mewling nonsense that one viewpoint is not science and is in fact anti-scientific.
(Actually, I have been out of the lab for well over 15 years, so it is technically not correct to predicate my first sentence with "As a scientist.")
The first starting point is scientific only if it comes with no consequences (God would have/would not have done X). And if it comes with no consequences, then it's a somewhat pointless assumption, isn't it? It's the ultimate violation of Occam's razor: assuming an entity that makes no difference at all.