Why does a sitemap ingore the «Use Categories Path for Product URLs» option value

Hello, I’m having an issue in that our Magento version 2.1 doesn’t care about the option

‘Use Categories Path for Product URLs = yes’

While generating the rules does work, products now have their full path URL e.g. /products/pet-food/kibble.html this isn’t respected in the minicart (link shows as /kibble.html). Frustratingly, these URLS (no category path) still work and create duplicate pages in SEO for us…

The same is true of our sitemap and breadcrumbs, they all use the shorter url and not the long one.

Any suggestions appreciated! Ii’ve dropped all rewrite rules, saved them again by re-saving categories, i can see them in the table…

It is intentional behavior, the same as in Magento 1.x.
A product in Magento could belong to multiple categories, so there is an ambiguity: which category path should be used for a product if the product belongs to multiple categories?
So Magento does not use any category path at all.