This is also true even if the actual rules of the universe are accessible since we can never be sure that this is in fact the case or that the rules we have are the fundamental ones.

Quite so. There will just be a greater absence of evidence for the supernatural if we find natural laws that make predictions that always match our observations perfectly. E.g. in a discrete universe (say Conway's Life) beings would be able to exactly reproduce the phenomena they experienced, although I am not sure what limits on measurement might exist in a discrete universe.