There were photo reconnaissance units in England to take the kind of pictures that they wanted to try to find the submarine pens and no need for the bomber units to try to find them on their own. The reconnaissance aircraft were able to fly at altitudes in excess of 40,000 feet and virtually immune to fighter interception.
When the call goes out of fighters at 10 O'Clock high, the German aircraft shown are fixed landing gear Junkers Ju-87 Stuka dive bombers. Due to high losses during the Battle of Britain, the Stukas were withdrawn from service in northwest Europe and would have had a very hard time trying to intercept B-17s since they both flew at around the same speeds and the B-17 was more heavily armed than the Stuka.
Major Stovall was never grounded in Season 2 due to poor eyesight. In Season 2's Storm at Twilight (1965), there are questions about his eyesight and he nearly grounds himself, but eventually returns to combat as Colonel Gallagher's co-pilot and brings the aircraft home when Gallagher is wounded, after which Gallagher tells Stovall, "Harvey, when this is all over, you can fly me home!"
The colonel who flew the sub pen raid instead of Gallagher is wearing pilot wings, certainly not command pilot wings as he was referred to by the general.