This is just like in Gundam. All gundams from RX-78 to F91, coexist in the same world. Just like the old gen Riders.
But, came a series of alternate reality Gundams like G Gundam, Wing Gundam etc, which has no connections or whateoever with one another, no matter the storyline, the cultures etc. These are like the new-gen Riders.
You cannot bring together 2 seperate populations together. It would upset the balance.
As in, Earth-1 (sorry, DC comics) has xxx humans and Earth-2 has the same number of humans. If brought together, then it's double the population, when put together. And what about buildings that were of different worlds yet on the same location?
This is why Crisis of Infinite Earths happened.
It is to eradicate anomalies and end confusion.
But of course, in Decade's storyline, it's more unique, as in, even the old-gen riders were thrown into seperate worlds. So, it's not surprising that Black will have to battle Amazon for the sake of their own worlds and the people they love.
They are not doing this willingly. But they have to. The rule's a bitch. Even if there's a better way, like assimilation, it's still no different from being eradication, because you're a new life form, with no prior memories. Imagine a Wataru-Kazuma hybrid.
Would you yourself allow such a thing happen to you? Of course you'd fight to stay alive.