As far as the issue goes, it doesn't really bother me. I doubt they will ever put Joker's real id out there. It's just another twist to the Batman/Joker story. If they both know who each other really are, then that's that. All the cards are on the table. It's still Batman vs Joker. Same as always.
But this right here nails it...
They're the exact same thing. And total opposites. At the same time.