I do not think that much "pure" exploring actually goes on in mathematics. If that's what mathematicians were really doing then why would they not just explore arbitrary axiom systems? Mathematicians typically identify two strands of mathematical work: theory-building and problem solving. In reality, these are not completely separate from each other. A theory may need to be built in the service of solving a problem and vice versa. As an example of the former, consider the P=NP problem. Someone notices that although they cannot prove a separation directly, they can if they introduce a modified model of computing with some funny class of oracles. After that, they start exploring this new model, partly because it is expected to eventually tell on the P=NP problem, but also perhaps because it has its own internal elegance and might have practical applications different from the problem for which it was originally invented to solve. I think the vast majority of exploration/extrapolation is of this type. It does not exist in a vacuum, but is closely tied to the existing structure of knowledge and the existing goals of mathematicians.
You are right that there are other processes going on in the knowledge network other than the replacement of analogies with new hubs. The latter would be a process of pure theory building, whereas in reality there is a mix of theory building and problem solving going on. I emphasized the theory-building process primarily because I think it is key to explaining why abstract mathematics shows up in physics. But for my explanation to work, I have to argue that the other processes that add new nodes, like problem solving, do not screw up the scale-free structure of the network or my argument.
I think it is plausible that problem solving adds new nodes to the network with a preferential attachment mechanism, so it is an example of the usual type of process that generates scale-free structure. To see this, one needs to again recognize that knowledge growth is a social process. If you are trying to prove a new theorem, you are much more likely to use techniques and ideas that come from network hubs rather than from more obscure parts of the network. This is because you are much more likely to know the contents of a hub, and also it is easier to communicate results to others if you can express them in a common language, and the hubs are the most commonly known parts of the network. (To see that this effect is real,just consider how much mathematicians complain when asked to verify a ~100 page proof by an unknown mathematician who claims to have solved a big open problem, but does so entirely in their own personal language and terminology.) Further, in collaborations between different researchers, the researchers are much more likely to have hub knowledge in common than anything else, so these methods will get used first. Thus, you are always likely to try ideas from hubs first, so new results are much more likely to get connected to hubs rather than more obscure parts of the network. This is nothing other than preferential attachment, which is the classic mechanism for generating a scale-free network.
So, I don't think that adding other types of mathematical exploration will change the structure of the network. In fact, it gives a better theoretical argument for scale-free structure than the process described in my essay. However, what these processes do change is that now not all the nodes at the edges of the network are directly connected to empirical reality. I still don't think this changes much. Theories are now built out of regularities in regularities etc. both in empirical reality and in the consequences of theories generalized from empirical reality. It is still no surprise that such theories should be useful for describing empirical reality.
Finally, I think that higher physics does have a big influence on at least some fields of mathematics. One just has to read Peter Woit's essay to see that. However, it is fairly unsurprising if some ideas in number theory that were originally motivated by quantum field theory later go on to have applications in quantum field theory. There is definitely a two way street. However, the more surprising thing is how often abstract mathematical ideas that at first seem to have nothing to do with physics later show up in physics. Gauss, Reimann, et. al. got the essential ideas of differential geometry right a long time before GR. Einstein simply had to allow for non positive-definite metrics to adapt the theory to spacetime. Since that time, people may well have used GR as inspiration for new ways of doing differential geometry. I am not an expert on that, so I don't know. Regardless, the main thing we need to explain is why differential geometry showed up in GR in the first place, and that is the type of thing I am trying to account for.