Questions
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Problem: Magento prioritises product URL's without categories?
Not to muddy up the conversation too much, but I wouldn't try to keep the category paths in product URLs as the canonical. What happens when you have one product in multiple categories? I would make .com/products/product-name as the canonical URL in the rel canonical tag. What you choose to show in the URL bar for the purpose of user experience and breadcrumb consistency is a different story. I hope I am understanding your situation correctly.
Intermediate & Advanced SEO | | Everett0