I can confirm that you’re correct in your assessment - Community Store isn’t built with multiple sites in mind off of the same install.
It handles multiple languages, with ways to translate products, etc.
But handling different actual sites, with different currencies and payment methods, would be very complicated. I can see how it would be useful, but nearly every aspect of the store would need consider multi-site configurations, everything from product prices, some products being available in some sites and not others, discounts being applicable to only one store, reporting on different sites… etc, etc…
So the path of least resistance is to just set up multiple sites/shops (perhaps building the first one and the cloning it), and considering a way to streamline product management via the API or similar.