Yes planes can pass over any zone that contain enemy ships, enemy planes, or enemy units. Planes cannot pass over neutral countries. In sbr’s they have to fight their way in if escorted or not if they are intercepted. After the interception or not then they get shot at by aaa and then if they survive that they get to bomb the factories and the tac bomber’s can bomb the airfields and naval bases. You are right that in the older version the aa was always active but not anymore. Hope this helps! :-)
Bonus clarification
-
US bonus:
U.S. controls the continental US and Mexico
(does this inlude SE Mexico as part of Mexico?)my interpretation is no
Allies control 5 of the 7 following islands. Midway, Wake, Marinaras, Iwo Jima, Caroline, Solomon Islands and Guam.
U.S. controls the Philippines.
U.S. controls Hawaii, Alaska, the Aleutian Islands, Line Islands, and Johnston Island.
U.S. controls Southern Mexico, Central America (Panama)and the West Indies -
SE Mexico is in a different NO, so you don’t need it in the first NO.