Ok, so here's how I understand this. Please correct me if you see any fault in my logic.
Zeb says: "Enemy ships inside your firing arc that you are touching are not considered to be touching you when either you or they activate during the Combat phase".
An excerpt from Phantom card: "at the end of the Combat phase, it (Ghost) may perform an additional attack with an equipped Turret".
The key piece here is the "end of the Combat phase" part, because it translates to "outside regular PS-order Combat phase activation of this ship".
Meaning that unless some rule would be saying "the ship is considered active when it performs additional attacks, even if those occur at the end of combat phase", Zeb can't be used for the Ghost/Phantom second turret attack .
Looks like you are right on.