The idea of the entire force having the F-35B is that it allows a surge capability to be able to fully man both carriers whilst still allowing training at home and roulement to take place. The aircraft and landing systems on the carriers supposedly allow currency to be maintained.
Accepting that the F-35A may be more closely matched to the RAF role, the ability to surge the aircraft to sea would be lost. It may never be needed and the aircraft may spend the vast majority of their life in theatres such as Afghanistan, but the capability will be there.
The balance between flexibility and performance would seem to be tending towards flexibility.