The atheist and theist both say "this is a possible explanation for what happened and is the best we have so far, so we'll use it as a hypothesis until something better comes along". The theist adds to that "... therefore God done it". The point is, there is no proof of God in the hypothesis, it is, as you say "God of the Gaps".

The theist argument that there must be a reason for everything and the reason is God confuses reason as cause with reason as purpose.