Christian mystical theology has never had a problem with the god of the gaps argument. It's always postulated that God was something so utterly alien from us (prior to time itself!) that we can know him only through revelation. The nature of God lies in the realm of the unknown, for our finite minds cannot grasp the infinite. Knowledge of God is given only through experience and his grace. What has been revealed is logic-defying and mind-bending, although it has a certain paternicity of its own.
Whether the God of the Gaps points you towards atheism or theism depends on your concept of the unknown. If you think of it as a fixed sized bucket of things gradually trending towards zero due to the effort of science, then you are an atheist. If you think of the unknown as practically limitless in size and our process of discovery as barely scratching the surface, then you are pointed towards theism. Generally, materialists trend towards the former and phenomenologists towards the latter.
As the wikipedia article stats, the idea was proposed first by Christians rather than skeptics, arguing that it's a weak form of faith, so you're definitely right on that point.
> Whether the God of the Gaps points you towards atheism or theism depends on your concept of the unknown
I really like this assessment. Looking at the sibling comments here, most seem to think all questions will be answered eventually, but I suppose that's impossible to know, since we don't even know what all the questions are yet.
Whether the God of the Gaps points you towards atheism or theism depends on your concept of the unknown. If you think of it as a fixed sized bucket of things gradually trending towards zero due to the effort of science, then you are an atheist. If you think of the unknown as practically limitless in size and our process of discovery as barely scratching the surface, then you are pointed towards theism. Generally, materialists trend towards the former and phenomenologists towards the latter.