The Comp has an E5 aluminum frame, carbon seat stays and a FACT carbon fork. The Elite has an A1 Aluminum frame and a carbon fork.
The E5 aluminum frame is supposed to be an upgrade over the A1 aluminum frame which, I'm guessing, means it's lighter while being more durable. The carbon seat stays should add some comfort to the ride. I couldn't tell you what the difference is between the FACT carbon fork and the Allez carbon fork.
Outside of that, it appears that both have the same components and wheels. So, it looks like you're paying $200 more for a lighter frame with carbon seat stays and a better fork.