It's possible to start tightening up a screw when it's not on its thread properly. And to start with, it all seems to be okay. It gets nice and tight, and it seems to hold properly. But you're wrecking the thread, and weakening the join. It wouldn't make the seal watertight, no matter how much you tightened it - if you were fixing a radiator on, or something.
How do you deal with this? The only way is to undo it and start again, and hope that you haven't already wrecked the thread.
What happens with naturalism, I think, is that the believer tightens the screw up when they haven't aligned it with the thread properly. It only seems to work. I don't think they end up with a watertight join.
Where naturalism breaks down is:
a) in epistemology - whilst it seems to the believer to work, you can't really know that there is anything else in the universe other than your consciousness. Descartes' famous "Cogito ergo sum" allows the observer to infer their own existence. However, it immediately means that the observer is unable to draw safe conclusions about anything else in the universe - everything else in the universe may simply be a product of the imagination of the observer, if you start from the observer.
b) in evidence (which is where ID comes in) - I think that the evidence, inferred through the scientific method, presented by ID proponents shows that naturalism is insufficient to the task required of it - which is to present a consistent metanarrative - a consistent explanation of everything.
A worldview is bound to seem pretty solid, and philosophical naturalism does work, in large measure. But it doesn't work well enough.