“Invent a new version of the universe” is normally not
    permitted by the software protocol, which is why this
    involves a client update and a hard fork.

To have "separate universes" is to have separate blockchains with different genesis blocks. There's an incentive to do just that with Ethereum[1] since the effective doubling of funds (X ETH on each chain) is bound to cause disruption.

Anything other than a new fork is going to fail for the reasons the author mentions.

[1]: https://reddit.com/r/etheregen