Is this issue possibly related to a defective damper? (Fox Evolution 2013) I have a 2013 Fox Evolution fork on my bike (bought new by me) that is subject to recall due to some forks having defective dampers.

I've been riding with a suspension fork since 1996, and I have never had a fork that tops out like this one. It tops out with a ridiculous clunk when I pop a curb, it tops out the same way when I ride down a bumpy trail. The rebound control knob has never seemed to have any effect on the rate of rebound.

I was hoping that the damper repair would fix the top out. So I took it to my LBS for the recall damper repair. 

They called me after 10 days and said, "it's topping out a lot, we think we must have got a defective replacement damper, we'll order another replacement damper." 

They called again after another week and said, "Damper is all good, still topping out a lot, we think there is some air that leaked into the negative air chamber, you need to take it to a specialized suspension repair shop for repair."

Is there any reason to think this is a warranty issue, or should I just cough up the dough for someone to bleed the air out of the negative chamber (which is what the guy said I needed to do)?
While it can be related to the damper, if 2 new dampers have not fixed the issue, as you describe, it is likely related to the SPECIALIZED BRAIN mechanism in the fork. 

Take it to a Specialized dealer. They will repair or replace it. And should do so at no cost or minimal cost.