OA,
Partially true. We release a percentage of sorties to the JFACC but definitely not all and very few if any rotary wing sorties. The "boat squadrons" aboard the CVNs are under USN control and they are usually fragged via the ATO. Gators usually are tasked and commanded outside the JFACC as well.
Please do not confuse reporting sorties to the JFACC so they can be coordinated with being tasked and commanded.
Allied Farce is a simple analogy. The USMC units flying out of Aviano were tasked via the ATO. The units flying off the CVNs had some of their sorties fragged via the ATO under apportionment, while the MEU (to include the ashore KC-130s) kept all their sorties and coordinated via the ATO.
There are very real disagreements on the JFACC/ATO process and employment. One philosophy is that air is to support someone or something and the other is that air is its own separate and distinct entity. The first will have CAS stacks, HVAA positions, and UAV sorties designed and oriented on the ground forces with the operational concept of what are those being supported trying to accomplish and how can we best support. The latter ends up putting CAS stacks, HVAA, and UAV sorties in places that people asking why as it provides far less than optimal support to friendlies and far less threat to the bad guys.
S/F, FOG