Not supporting the arguement one way to the other but it might make some sense to have the JCA in just one colour. To have, say, two different colours on one ship will inevitably lead to confusion. As long as the light blue is fed from the wider air force they will always speak a different language.
OTOH a larger pool of pilots increases the number available whereas the RN pool will inevitably be smaller and also single role, on the assumption that there is no cross-over RW-FJ.