It seems that the version of evil Superman which Captain Luthor is desperate to stop our Clark from becoming was, indeed, a real Kryptonian who used his power for his own gain, so it makes complete sense that once Luthor was integrated into this new multiverse, he’d assume that any Superman is a bad Superman.
At the end of that event, literally everyone and everything was destroyed for a time, until Oliver Queen and the Paragons were able to create a new multiverse and bring people back, but with a lot of changes.