In any formal system, you need to have undefined terms, i.e., terms that cannot be analyzed in simpler terms. Otherwise, you will never end the explanations. So, the easiest answer to your question

I want to know what a node actually represents in rule space

is that the nodes and the hyperedges are undefined terms from which everything else emerges. It is like the strings in string theory: they are not made of something more fundamental, they are the most fundamental objects in their theory. Nevertheless, this status does not exclude the possibility that the nodes, if they exist in nature, may have internal structures. If this is the case, then a more precise theory could be developed in the same way that the theory of quarks was made in order to express the internal structure of protons, neutrons and other particles.

That's the phase transition between primordial chaos and primordial order. Rulial rain on an endless ocean of half computed universes and primordial order icebergs.

Michael:

I wish I had an answer for you. But when you figure this out, there might be a great sci-fi story to be told about these nodes and edges.

I won't be surprised if the new Wolfram Model has some of the secrets.

But to be fair, we already know the answer is 42. But we have to figure out the question.

Just remember to bring your towel with you.