Well I don't know exactly. I had 3 different repairs under AppleCare (screen flickers, bad RAM modules and GPU died). I went in due to logic board failing 3 months after my AppleCare ended. The Genius looked at my repair history and stated that he was going to give me the flat-repair option.
He explained it was basically a detailed repair process where they got my Mac, started figuring out what was wrong and swapped anything bad (except battery). I agreed.
In the midst of all this he saw that I didn't have the original 250GB HDD my Mac brought. I explained I had replaced it since my brother dropped the HDD when I was performing a HDD diagnosis using my Mac for a friend. Genius told me to swap out my WD Black Scorpio drive and put in the damaged drive if I still had it (lucky me I still did). I got that replaced & upgraded from 250GB to 320GB.
Apple repair and/or replaced HDD and logic board. All for $230. In the end, the flat rate fee option will most likely depend on how much issues you've had. For me, it is true I had 3 big issues, but Apple was very direct with me and told me they messed up and did it right. Which is why, my next computer will be a Mac (assuming they keep dGPUs in there).