The first step is to create Networks inside a Multisite Network. And it can be done with:
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Networks+
This plugin provides the interface to set up another network of sites within the install you already have. You may choose to run this additional network off a different domain entirely or a subdomain – it’s very flexible.
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WP Multi Network
Adds a Network Management UI for super admins in a WordPress Multisite environment
The second step (out of the scope of a Q&A site) is to inspect these plugins for public functions/methods and hooks to integrate with your custom commerce solution.