Rationalist arguments against God-in-the-gaps are useful for ferreting out an idea of God that really does need to go: God as a first cause in history. It’s a fine myth and a terrible theology.
By now we’ve had four hundred years of gods who needed to get some natural process going: the Newtonian god that had to hit the planets with just enough finely-tuned force to put them into orbit; the pre-Darwinian god that had to make sure that someone put the chickens and the worms in the same ecosystem or needed to make sure that the chickens were given beaks that could pull out the worms; now there are arguments for the god who needed to form some first living cell, announce the Big Bang into existence, tune up the gravitational constant, decide that ice should have a greater volume than water, etc.. If we could only go far enough back in time we could see God at work! He’s got to be back there somewhere!
The argument is about as good as one that would claim to find God by zooming in on some area. How much resolution would it take to see all the little divinions at the bottom of things!?! He’s got to be down there somewhere! Whatever begins to exist must have a cause, right? So matter has to begin to exist at some point, since under that threshold there must be nothing.