I stand by the idea that SYNTHESIS is more than just the head, the name alone suggests it is the first part of the reunion. The later bosses indicate the final steps in the reunion, after merging with Sephiroth (one of the last main sources of Jenova left to be joined).

As you said Jenova's power are largely passive (though she's still damn tough physically). Doesn't this suggest though that instead of Sephiroth being the brains behind the muscle of Jenova, it was in fact the other way around?