Shop Based Permalink For Taxonomy

WordPress permalink are matched using a list of regular expressions which are matched in an order defined by their priority.

Because changing the custom taxonomy to be prefixed by /shop/ causes the conflicting paths to return a 404, my suspicion is that the built-in URL structure is matching, but then not finding the custom taxonomy within the default product category terms.

This is not an especially simple thing to resolve:

• It may be that moving the custom taxonomy permalink rule to a higher priority will resolve the issue. This might also cause built-in product categories to 404. Testing this would require using a plugin like Query Monitor to see which rule is matching, then filtering the priorities.
• A complex solution would be to deregister the product category default permalink rule as well as the custom taxonomy rules, then write a new rule which checks both taxonomies together.
• A simple solution might be to extend the 404 template or use the 404_template filter to redirect to the default custom taxonomy URL if an expected URL is accessed under /shop/

Each of these approaches gets technical very quickly. There may be a permalink plugin available, either for free or as a paid resource, which can handle the requirement, but generally one might need to find a system sophisticated enough to query two different taxonomies for a match within one URL structure, which usually requires unregistering the default permalink rules, then writing a custom rule which queries both taxonomies for a match to the requested URL.