Hello, @subsjerry
First of all, I would like to mention that there is no need to manage two separate Magento systems. You can manage everything from one website and connect pages by the alternate tags. There is the Magento 2 Altertage Hreflang Extension by Magefan. which allow you to set the alternate tags for each Magento 2 page connecting them and letting Google know which page to direct your customers too. This way you avoid the duplication issue.
There is also an option Locale Depends on Region, which is useful in case you manage store views with the same language which has variations. ( e.g. when you don't want your English readers from Australia to be shown the same content as English readers from the USA depending on some material relevance).
Here is a video where you can see how it actually works to make sure if it is what you are looking for:https://www.youtube.com/watch?v=_dNAErMCUfA&t=15s