Hallo!
I am new in this community and in this discussion, in particular. CA modelling of fundamental laws of physics is very interesting to me. I think NKS is full of exciting ideas which I study and try to reconsider step by step. During reading NKS I imagined that CA could be a link between physics and a model I had considered previously. Please take a look at my preprint https://arxiv.org/abs/1705.04376 which presents a link between an extended model based on CA ideas and some outcomes which can be non-trivial for physical systems.
Please excuse that my model is loosely connected with yours but the idea of modelling basic physical objects is common. I hope that my comment could extend understanding of physical properties which you are writing about. I hope that the graph geometry which you are considering can be related to a 'geometry' of relations which I have presented in the mentioned paper.