They already explained away the JFK bit. He was lost in time so Superman met JFK while he was there. It's not like Superman travelling in time is a new concept that Morrison needs to introduce, is it? What more explanation is necessary?
DC has explicitly said this story will be in continuity, so there's no question about that, and they've also said that PKJ will explain how Superman got old and lost his powers, so everything will be explained. They just aren't going to do so right now. The original plan was for the miniseries to come out much faster than it will now, so we'll have to wait a little longer, but it's not like an explanation isn't coming.
I mean, we all know that DC underwent a lot of editorial turmoil over the last year. Given how AT&T stripmined them, I'm not expecting everything they put out over the next few months to sync up perfectly. As long as the story's good, I'm happy. Superman & The Authority #1 was a fun comic.
Wouldn't you rather be able to read Morrison & Janin's story now or do we all have to wait a few months so we can read how PKJ's story that explains it all, which might very well spoil some of the surprises that Morrison has cooked up?