Yes, there is of course randomness that will be introduced into the system from the real world. I should have said if both systems receive exactly the same inputs (which is probably not very practical in many scenarios).
I should point out that I don’t entirely understand what this is trying to gain WRT the original topic. One could just as easily train up one single HTM system with the controlled inputs, study and learn some information about its internal representations, and then copy it into any number of instances.