I swear, the big reason models are black boxes are because we _want_ them to be. There's clear anti-sentiment mentality against people doing theory and the result of this shows. I remember not too long ago Yi Tay (under @agihippo but main is @YiTayML) said "fuck theorists". I guess it's not a surprise Deep Mind recently hired him after that "get good" stuff.
Also, I'd like to point out, the author uses "we" but the paper only has one author on it. So may I suggest adding their cat as a coauthor? [0]
Because the synthetic linear languages are computationally/structurally simple LLMs will, unlike humans, learn them just as easily as real human languages. Since this hierarchical aspect of human language seems fundamental/important LLMs therefore are not a good model of the human language faculty.
If you want to refute that claim then you would take similar synthetic language constructions to those that were used in the experiments and show that LLMs take longer to learn them.
Instead you mostly created an abstraction of the problem that no one cares about: that there exist certain synthetic language constructions that LLMs have difficulty with. But this is both trivial (consider a language that requires you to factor numbers to decode it) and irrelevant (there is no relation to what humans do except in an abstract sense).
The one language that you use that is most similar to the linear languages cited by Moro, "Hop", shows very little difference in performance, directly undermining your claimed refutation of Chomsky.