Cant answer the cities bit yet till I play game again but there werent that many neutral countries during ww2
France was in at the start with Britain so most flights would have gone over France to Germany
By early 1940 most of europe was under german control so any flights out of Britain would have been over the war zone anyway
While there were a couple of neutral countries left no doubt flights did stray in their airspace from time to time and no doubt they complained but most of Europe at the time was in fear
Apart from the German western offensive there was the Russian/Finland war with Russia being a member of the Axis along with Bulgaria, Croatia, Hungary, Romania & Slovakia as well as Italy so by the time you add in the countries under German control there werent that many neutral countries to fly overand by the end of 1940 the vast majority was under the jackboot ( map is 1942 but Europe pretty much the same from August 40 except for Russia joining the allies in 41)
Trouble with the game is the engine is too rigid - If Neutral countries were to open fire on aircraft in their airspace they would have to be classed as an enemy of that country to do so and that would lead to neutral shipping showing up as an enemy