So, sorry, but this is still unclear to me - which were the real
squadron staffs - these still flying Tomcats, or those already
transitioning to Rhinos? I guess the latter was finally replacing the
former, so indeed, not all aviators were transitioning...

The delivery of a squadron's-worth of F/A-18E or F takes time. The first
examples you see are usually flown at VFA-122 to train whatever Super Hornet
pilots are on the pipeline at the time. When the core pilots of the
transitioning squadron are back from deployment, a few more birds will
hopefully be available, and the squadron will begin to take shape, under the
RAG's wings. Things start to get "ship-shape" when they get their
safe-for-flight certification, which means they will be responsible for
their own flights henceforth.

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José Herculano