But in the hypothetical where both the axis powers and the allies have less personnel there wouldn’t be as many pilots navigators etc for those bombers.

Actually in your example the defending forces come out on top, even if the level of conscientious objection wasn’t symmetrical. A ww2 era bomber required several crew members (pilot, co pilot, radio operator, navigator) whereas fighters just needed one person.

In this hypothetical, the effects are not symmetrical even if the reduction in military manpower is symmetrical. Britain lacked trained personnel more than materiel; more civilians would have exacerbated that problem. Germany, on the other hand, lacked both in the real world - in a situation where fewer civilians agreed to military service, their materiel disadvantage would have been lessened, while their personnel disadvantage would have remained proportionally steady to Britain's. Britain, primarily on the defensive in the air during those early days, also would have fewer troops to man air defences across the points where German air attacks were most likely to target or cross; and Germany, on the offensive, would suffer from fewer disadvantages as concentration of force in an offensive, especially in air campaigns, is most often bottlenecked by logistical concerns, rather than manpower concerns. As an additional consideration, manpower constraints would have favored highly destructive air campaigns which generally kill more civilians than soldiers, over ground campaigns which generally kill more soldiers than civilians.