Something Jay Richards wrote a while ago (I think it was here, though I 'm not sure) that I finally got a handle on. I remember him talking about trying to determine if something is designed and focusing on the foreground instead of the background. I don't remember him offering an example, which I think would help. I just happen to have one:
We can look at a painting and focus on different aspects of it to determine what was designed (by humans) and what wasn't. First, we can focus on the material of the canvas, and decide whether that was designed. Then we can focus on the paint, and determine whether that also was designed. Then we can focus on the actual pattern of the paint on the canvas and determine whether that was designed as well. We might decide that the actual pattern of the paint wasn't really designed by anyone (it was caused by some open paint cans spilling there contents on the canvas , when a tornado caused the shelf to fall over). This does not mean that we don't think the canvas and the paints were designed.
Likewise, when Theists want to determine what God designed, we can focus on the laws of the universe, or on the material that makes up the universe, or on the various objects in the universe. We might decide that God created the laws and the material, but that the objects in the universe were produced secondarily by the laws and the material, not directly by God. Or we might decide that God also directly produced some or all of the objects in the universe as well.
ID typically focuses on the foreground of the origin of life and its development and argues that it was designed by somebody (most IDists are Theists and usually think that God is that Somebody). But if someone could show that ID is mistaken, this does not mean that arguments that God created the laws of the universe, or the material that makes up the universe, are mistaken. But if ID is correct, then there is additional evidence for God. Not only must the existence of the laws of the universe and the material in it be explained, but also the origin and development of life.
So when I hear theistic evolutionists or Thomists object to ID, that somehow it puts at risk the case for God, my answer will be: you've lost your focus. The case was whatever strength it was before ID came on the scene. ID cannot weaken it. It can only strengthen it.