Drupal Commerce has many models and relationships. This page provides explainations as to how these different models related, including entity relationship diagrams.
Orders will only ever have one store, and it is stored as an entity attribute.
Products, by default, have an entity reference field that targets stores and allows one or more stores to be selected.
Stores are fieldable content entities (not configuration entities) that contain a lot of information about the physical location of the merchant. By default stores collect the following:
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