Reason is the tool of science, so it is the limits of reason that I am addressing. This is a more precise formulation of what I am trying to talk about. So, I take the question to be whether or not reason is limited in some way. We are concerned here with the inquiry of how did the universe come to be, or an inquiry about causality in ultimate terms. I don't think this can be concluded to the satisfaction of the intellect by trying to construct a chain of cause-effect. Are you suggesting that it perhaps could be, that there could be some answer of the thought-reason-language type that would conclude the question of the ultimate origin of the universe?

"But if you manage to produce a mathematical model of quantum emergent spacetime, I am not sure any of the underlying model elements will be observable in principle..."

I think this situation will be unsatisfactory to the intellect and it will try to somehow model the unobervables. Each stage of the inquiry and model building can only lead to further questions... ad infinitum.

As I have said before I believe that science/reason is immensely valuable, its just that as a tool or mode of knowledge I believe it has definite limitations, which if not spotted could cause confusion and madness. Some inquiries are just not amenable to reason, but there are other ways too.