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.

This allowed experiments where the frequency of light was varied continuously, by rotating the prism.

Moreover, already during the first half of the 19th century, it became known that using gas-discharge lamps with various gases or by heating certain substances in a flame you can obtain monochromatic light corresponding to certain spectral lines specific to each substance. This allowed experiments where the wavelength of the light used in them was known with high accuracy.

Already in 1827, Jacques Babinet proposed the replacement of the platinum meter standard with the wavelength of some spectral line, as the base for the unit of length. This proposal has been developed and refined later by Maxwell, in 1870, who proposed to use both the wavelength and the period of some spectral line for the units of length and time. The proposal of Babinet has been adopted in SI in 1960, 133 years later, while the proposal of Maxwell has been adopted in SI in 1983, 113 years later.

So there were no serious difficulties in the 19th century for using monochromatic light. The most important difficulty was that their sources of monochromatic light had very low intensities, in comparison with the lasers that are available today. The low intensity problem was aggravated when coherent light was needed, as that could be obtained only by splitting the already weak light beam that was available. Lasers also provide coherent light, not only light with high intensity, thus they greatly simplify experiments.

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.

An environment living in Conway’s Game of Life could be quite capable of hypothesizing that it is implemented in Conway’s Game of Life.

Systems can hypothesize about themselves but they cannot determine why the rules they can learn exist in the first place. Prior states are no longer observable so there is always incomplete history.

Conway's Game of Life can't explain its own origins just itself. Because the origins are no longer observable after they occur.

What are the origins of our universe? We can only guess without the specificity of direct observation. Understanding is incomplete with only simulation and theory.

So the comment is right. We would expect to be able to define what is now but not completely know what came before.

"The universe is not required to appeal to your aesthetic tastes."

That presupposes that there's a bottom, and that each subsequent layer gets simpler. Neither proposition is guaranteed, indeed the latter seems incorrect since quantum chromodynamics governing the internal structure of the proton is much more complex than the interactions governing its external behavior.