I think what jancotton was saying was that once Zone 2 has been called, Zone 1 and Sky Priority can board through the Sky Priority lane. I used to see what you are describing where they call Zone 1 through general boarding and FOs are in Zone 1 but could jump to the front of it by using the Sky Priority lane. On all my flights recently, the gate agent has specifically instructed Zone 1 to use the Sky Priority lane.

In one such instance, I was #1/1 for 1 FC seat on a DCA-ATL segment that hadn't cleared when boarding started. I got in line to ask the agent if she could clear me. While waiting, I heard her say to the other agent "I'm going to clear the upgrades" and looked up at the screen to see my name cleared. At this point, Zone 1 had been called through Sky Priority lane and there was a huge line. I went up to the rope across the General Boarding lane and told the agent scanning boarding passes that my upgrade had just cleared. She made me go to the back of the Zone 1 line. This wasn't such a big deal in this instance, but I'd be quite annoyed and might have argued if I was a late-arriving FC or GM/PM/DM customer who was forced to wait behind all of Zone 1 because they were boarding them (us) through Sky Priority. What if it caused one to miss out on a PDB?