Typically whenever you look closely at an object with complex behavior, there is a system inside made of smaller, simpler objects interacting to produce the complexity.
You'd expect that at the bottom, the smallest objects would be extremely simple and would follow some single physical law.
But the smallest objects we know of still have pretty complex behavior! So there's probably another layer underneath that we don't know about yet, maybe more than one.
Yeah that's the outcome theorized by Gödel.
Incompleteness is inherent to our understanding as the universe is too vast and endless for us to ever capture a holistic model of all the variables.
Gödel says something specific about human axiomatic systems, akin to a special relativity, but it generalizes to physical reality too. A written system is made physical writing it out, and never complete. Demonstrates that our grasp of physical systems themselves is always incomplete.
I agree, and I think that your claim is compatible with the comment that you are responding to. Indeed, perhaps it's turtles all the way down and there is systematic complexity upon systematic complexity governing our universe that humanity has been just too limited to experience.
For a historical analogy, classical physics was and is sufficient for most practical purposes, and we didn't need relativity or quantum mechanics until we had instruments that could manipulate them, or that at least experienced them. While I guess that there were still macroscopic quantum phenomena, perhaps they could have just been treated as empirical material properties without a systematic universal theory accounting for them, when instruments would not have been precise enough to explore and exploit predictions of a systematic theory.