I think any justification they make to differentiate between god and your gnomes will eventually be shown to rest on the cosmological argument, which is why they will feel justified in believing in god and not the gnomes. The problem is that I have never even seen a Christian attempt to make the logical argument that the first cause is Yaweh without referencing the bible in a circular manner.
Even if the open windows of science at first make us shiver after the cozy indoor warmth of traditional humanizing myths, in the end the fresh air brings vigor, and the great spaces have a splendor of their own - Bertrand Russell