1. All of the universes in the registry are currently selected by hand. We basically selected the ones we thought looked interesting during the various searches we have done. We are going to have a more rigorous process in the future, where we will have automatic tests for whether a given universe is consistent with known physics.
2. See (1).
3. See (1).
4. It's a truncated hash of a canonicalized rule with the number of digits chosen based on the complexity of the rule and to avoid duplicates (initial condition will be a separate number if non-trivial).
5. It's an Automatic value for the number of steps argument of WolframModel. You can check the source code here.

Good point about the notebook naming. I have forwarded your suggestion to the registry developers.