Certainly, there can be remote and proximate causes of the same event, although in this case the proximate one covers not just human history but the evolution of life and of the solar system, and so on back to the big bang. Unless we're positing that God intervened miraculously within nature, as the religions themselves do maintain (e.g. God gave Moses the tablets or he copulated with Mary to produce Jesus), the religious "explanation," that God got the universe rolling in the first place, is hardly as substantive as the secular one.
But I agree that there can be different kinds of explanation, or at least that begging the question in the scienstistic manner makes for a cheap victory. However, we should be clear about the type of explanation we're providing, and scientists are clearer than theists. The best worked-out kind of explanation is the scientific kind, which means it might be better to use a different label for non-empirical "explanations." In providing only metaphorical or subjective truth, the latter might better be called therapies or artistic expressions. For instance, the idea that God "created" the universe would be a poetic metaphor, one that resonates with human sensibilities, but that isn't really an explanation of any kind. But that's a semantic question.
See the article I just posted today, by the way, about the problem with scientistic atheism. And I could cite a dozen more I've written that espouse a more "postmodern," pragmatic, neo-Kantian, humble view of knowledge.
