Thank you for the extended explanation Ben, it’s good to know this is the expected behavior. I guess what threw me was that it doesn’t match exactly. The option title “Shop base with Category” is crystal clear and gives exactly that in the “Custom” field (/shop/%product_cat%), but its description is:
http://web.my/sandbox/shop/product-category/sample-product/
which to my mind should have yielded a “custom” field of:
/shop/%product_cat%/product
based on the behavior of the other options.
Thank you for clearing things up for me.
P.S. Ok, after looking back at the menu, I realize that this is NOT what I should have expected, and ‘sample-product’ never generated any output in the custom field.