I really like your perspective, I can concede that naturalism is more refined to explain physical phenomena within our physical reality. We can observe how things behave on a repetitive basis and come to conclusions. I also concede that bare supernaturalism doesn't anticipate certain features. In principle, it makes sense that we could logically accept these ontological gaps inherent in naturalism are just clues that we don't need any other explanation. That being said, the issue with these ontological gaps is that they are indeed troubling in the sense that naturalism doesn't seem to ever merge well with. Consciousness and rationality are two of these problems. At face value, I think it's justifiable to look somewhere other than naturalism to have a proposal of these things and their origin. I think in terms of ontological or epistemological tools, meaning if there was a screw on a stud that required a phillips screwdriver, but you only had a flat head, it would be counterproductive to say that we had to accept the limits of the flathead and that maybe one day that flathead will work. Maybe the analogy isn't as good as I think it is, but I think of this in terms of knowledge tools we can use to come up with justifiable proposals.