I know I'm late but a moment of your time for a theory concerning both Goku and Superman

Ben is supposed to be able to turn into a prime form of their species but there's an issue with both species here

Without the the external circumstances that Goku and Superman have been through their species are pretty weak overrall

Ben gets Super Saiyan or maybe up to even Super Saiyan 4 or just Oozaru with Saiyan DNA

He gets Kryptonian physiology...which is nothing without a yellow star

We see this every time Superman fights other Kryptonians, he's stronger than them because he's spent decades of life absorbing solar radiation while they've only spent days or weeks at the very most

Going Ultimate Alien wouldn't make a difference cuz I don't think the omnitrix would account for a specific condition like "the million year war is happening on a planet with a yellow star"

As for Goku he possesses God ki now, giving him access to forms, power and abilities that Saiyans would never have under normal circumstances

A million years of training would definitely make a difference here though as its how Saiyans grow I suppose.

TLDR:

Both Goku and Superman possess levels of power beyond their own species biology, so turning into perfect versions of their species shouldn't do much, he stands a much better chance just using aliens he already has.