That "explanation" is an incidental story point, a stylistic choice. There have been countless prior reinventions that haven't had any such "explanation," and audiences haven't had a problem understanding it. Because most people are smart enough to know the difference between fiction and reality and thus don't need an "explanation" for how there can be two or more different versions of an imaginary concept..
Agreed. It's possible to overthink this and, aside from THE FLASH, none of the various superhero reboots have felt obliged to actually "explain" themselves via abstruse multiversal conceits from the comics--because there's never been any real need to do so. Most moviegoers understand the concept of remakes and reboots well enough--and don't require any sort of "in-universe" justification for it.
"Is this supposed to be the same Joker that fought Michael Keaton in that other BATMAN movie? You know, the one played by Jack Nicholson?"
"Nah, they started the series over in the last movie, the one with Katie Holmes."
"Got it."
I seriously doubt whether many moviegoers came out of THE DARK KNIGHT wondering whether it was set on Earth-1 or Earth-2 or groping for multiversal theories to explain why Heath Ledger was playing the Joker differently than Nicholson or Cesar Romero.
Sometimes a reboot is just a reboot.
