The Yoast SEO metabox can only be used on posts and pages that appear in the backend. So, if the page /store/store1/product1 is created dynamically, you won’t be able to use the Yoast metabox to change the canonical link (or other meta data) of that page.
That being said, you should be able to change the canonical of the page /store/store1. Can you please provide the actual URL of the page so that we can take a look? Additionally, it’d be helpful if you could provide a screenshot where we can see what canonical URL you’ve set in the Yoast metabox for that page.
Closed due to inactivity.