Indeed, the 40 figure is hangar storage only and not the maximum I believe, as is the practice on Royal Navy carriers. It's increased complement is 40 plus 16-20 deck parked aircraft, which is what the Royal Navy call "surge" deployments I think. USN carriers routinely deploy with aircraft both stored in the hangars and deck parked unlike the RN who only store aircraft in hangars, hence the greater size of the US air wings. Both carriers can comfortably operate three to four squadrons of combat jets. A figure of 60 as a surge complement for the QE could be arrived at by the physical size of the hangars and the deck parking capacity.
It should be noted that a typical air wing on a Nimitz is around 64 aircraft though it is capable of more. Also, given the surge air group of 60 compared to the maximum of 85 for a Nimitz (64 is more typical), the QE air group is roughly 70% of the size. Though, I believe the size of the air wing means little at such a small difference given that both carriers have a projected sortie generation rates of between 110-120 per day.
I'd be shocked if the RN didn't store on deck in the event of a major war.