It is absolutely crucial who exercises command and control of JCA.
The RN generically has neither the people or the kit to Command and Control FJ assets at either the operational or tactical level. To do so would require a DTIO and JFACHQ type set-up, afloat.
FJ assets need to be commanded and controlled by a CAOC working for an ACC. CVF should hopefully provide a very flexible platform from which to operate an array of the ACC's assets, but that is all it is.
Some land-based proponents need to just relax a little bit and accept that no-one is trying to steal aeroplanes and lock them in the hangar aboard CVF. Some maritime proponents need to accept that the CVF will never compete with a full-up airfield for scale and support.
In short, there will be occasions where an ACC will want his assets to be flying from a boat, and others when he won't. The key is that the RN cannot give anyone a career path that ends up as an ACC, and doesn't possess the kit to host a light-blue/ coalition ACC and his staff afloat.