Commerce Product with diffrent prices for different shops
To resolve the product display &lt;-> product issue, I'd be using Inline Entity Form to embed the product form right into the product display node form. However, that doesn't address your need to have hundreds of unique prices corresponding to different physical locations. That's another issue entirely that we would typically refer to as pricelist functionality.

We do have a Commerce Pricelist module, but since "Store" wasn't a core entity type in Drupal 7, there is no pricelist variant correlating to a store. You'll likely need to enhance that module yourself to make it "simple" for end users. Other options would be dependent on your greater site IA ... and it's worth noting that store based product availability and pricing would be better suited to Drupal 8 if there's any chance at all at upgrading.