Most of the bullet points you've listed can be summed up as "business logic." I'm sure the Stuxnet programmers worked with physicists and industrial controls specialists.
Developing software for, say, jet engines requires sophisticated knowledge of jet engines, which is probably about equally complex. But it's manageable because programmers work with engineers who are subject matter experts.
Developing software for, say, jet engines requires sophisticated knowledge of jet engines, which is probably about equally complex. But it's manageable because programmers work with engineers who are subject matter experts.