As I read the issue, it wasn't Superman's powers that altered reality; it was the environment he was in. Much like Superboy Prime didn't have any reality-altering powers, but the Paradise Dimension that Alex Luthor took them to did. And because of that, SBP was able to trigger changes by punching walls. In a similar way, it wasn't Superman's powers that blended the two timelines together; it was Red and Blue coming together in whatever the place was that Mxy had taken them to.