If a lack of an alternate explanation somehow is thought to provide support for an explanation of the natural world based on the supernatural, it is a flawed argument. That is what I meant by the God of the gaps argument assuming that we will not discover anything new about the natural world. Unless we make this assumption, we will not jump to a supernatural explanation. How is this an outdated view?
But see I think from the theistic view, seeing that there is a lack of explanation from both religion and science (after all all the "explanations" for adaptations are merely created stories and anecdotal evidence because no one was there to observe) we base our conclusion on the next most logical source, our personal experiences.
And for us those experiences line up with the truths in the Bible. When we combine both we arrive at the conclusion that it is more likely that there is an intelligence in the universe.
And really there is no logical inconsistency or God of the gaps arguments, we're talking about metaphysical concepts here and by definition that means there is a lack of physical evidence.