Are there deep, mistaken underlying background assumptions about the nature of reality that support our empirical sciences?

Here is a thought: I was talking to someone about qualia and causality when it dawned on me that an unexamined background assumption I had was the following.

“There is a basement reality.”

Quarks may ultimately break down into further components, but we are working under the assumption that there is a deeper, smaller set of actual building blocks. Even if you don’t postulate discrete building blocks, the background assumption of “a basement reality” is still present in the idea that the entire physical universe can be described in terms of fields and wavefunctions.

But couldn’t this be fundamentally mistaken? How? Here is a ridiculous example that drives the point home: Imagine that inside each fundamental particle you encounter a kind of miniature black hole, within which the entire universe is enclosed. The microscopic properties of those particles are the result of the angular disposition of the entire universe within it relative to the nearby particles. I don’t mean that “there is another universe inside it.” The idea here is that “inside each fundamental particle you literally, actually find the same universe within which the particle is supposedly contained.”

I say “supposedly contained” because this particular model would make it indeterminate whether the particles are in the universe or the universe is in the particles. In fact, neither description would be true, and you’d see a fundamental breakdown of the background assumption. You couldn’t reduce the behavior of any part of the universe to the behavior of underlying mechanisms.
How could this universe evolve? After all there is only so many possible self-consistent “solutions” to this fractal self-contained view of the universe. Things like that exist in math: The smooth morphing between nearby Julia sets. Each one of them is an infinitely intricate universe on its own, and yet you can find an arbitrarily similar set that is itself also fractal and infinitely intricate. You see sudden structures appear out of nowhere (quantum mechanics anyone?) for the simple reason that those things complete the fractal.

Are we a morphing fractal with no ground and no roof?

Implausible as it may seem, at least this view would make the question “why is there something rather than nothing” a *little* bit less mysterious. There is something ’cause it approximates nothing by not being based on anything ultimately real. A big mirage of nothing.