Well, to give you an idea of why the story worked like that, the anime is based off of a video game. And basically in the video game you have a FFX-2 like system where you can work to 100% completeness. The first After Story end Tomoya wasn't at 100%, so the final episode was him "replaying" and getting that 100%, which ends in a happy ending for everyone (except the girls who want to be with Tomoya). So I'm betting that works for the answer to most of your questions.
Yeah the flashback episode was pretty win, and it was nice to see a summary and prequel instead of ending on that big dramatic note. When an anime ends all big and dramatic I always want more and After Story supplied more right away, I liked that a lot.