It makes sense; if they have to change him, better to frame it as a big "event" that was entirely their idea than to admit up front, "We lost the rights to the real thing, but here's something we cobbled together from what was left." In a weird way, it's kind of reassuring to know Superman is still so important to them that they're willing to change the whole DCU to cover their tracks.
I'm pretty sure this is a big piece of what is going on. After all, why would DC give Superman an entirely new origin - just so they could reboot him 3 months later and give him
another new origin, erasing the one that they just gave him? The only way that makes sense is if it was the result of an unexpected decree from WB legal.