WooCommerce Amazon Fulfillment can only connect to a single MWS region with a single MWS / Seller Central account per WordPress installation (or site). However, larger organizations do exactly what you are talking about by using WordPress multisite with individual sub-sites per region, or by using individual installations of WordPress. The only straightforward solution to this scenario is to run unique individual sites per region, with unique Seller Central accounts per region, and WooCommerce Amazon Fulfillment installed on each one and connected to their respective MWS accounts independently. Naturally, those sites can be on subdomains or unique country targeted domains. In fact, this is exactly how some of our existing WooCommerce Amazon Fulfillment customers handle it. Here's one example of WooCommerce Amazon Fulfillment in the wild on multiple sites (multiple installs) connecting to distinct FBA regions:
Supporting multiple MWS regions from a single site is something we're looking into for the future, but there are lots of technical hurdles with that approach because of how Amazon's APIs work, having different inventory levels per region even for the same SKU, etc. In the meantime, we recommend using International fulfillment with FBA from a single home region, or having 1 site per region to connect to unique Amazon Seller Central accounts.