They are a better team now than they were then now that their young QB has grown up and their offense is on fire, but you are right. The regular season counts and they lost head to head. In fact, one of the things I like about NCAA football is that it's the only major sport where you have to excel during the regular season to make the playoffs.
Now, I don't really think they put Miami in because they beat Notre Dame head to head. The committee poll had Notre Dame ahead of Miami in recent polls because Miami had some bad losses and aren't a great team. I believe they flipped it at the end because they wanted to put an ACC team in there and it wasn't going to be Duke. If Virginia had beaten Duke, then I think Miami doesn't make it. There was a legit case for Miami over Notre Dame though.