Ah yes, good point. And Conway's Game Of Life is a better example because yes, indeed, gliders are fundamental (as are molecules). And Conway didn't make GoL for the gliders specifically, they may have surprised him just as much as us (although I'm sure he
was searching for emergent phenomena).
So yes I think there are certain initial conditions and rules that don't produce gliders/molecules, but that is only obvious either through simulation or hindsight. In the beginning, as a pundit, or a fly on the wall, it feels like there's everything to play for. So a weird thought experiment is if we could somehow contain a randomly-seeded, massively slowed down Big Bang and have modern day scientists (without recourse to modern knowledge) observe it. I imagine there'd be all kinds of theories, conversations, schools of thought, etc on which direction the universe would take.
So I think the point is that, in fact, we are observing a Big Bang! Just at a later stage. We're trying to understand what's happened and what will happen. A very prescient example of that is Fermi's Great Filter[1], ie does intelligent life necessarily destroy itself?
So perhaps I can summarise my original comment with the thought experiment of those scientists observing the impossibly contained early universe asking themselves in the same way we ask ourselves about the Great Filter, "are protons, neutrons and electrons, capable of stabilising into complex but harmonious structures?"
1. https://en.wikipedia.org/wiki/Great_Filter