Hi there,
the Theme doesn’t interfere with the permalink structure.
I did notice is if i visit the URL you want ie.
https://thegoldenlamb.com/resources/terms/r/ristretto/
Then it gets 301 redirected to the URL you don’t want – see here:
Not sure if you have any redirects setup on the site.
But creating custom permalink structures is best suited to a plugin like Yoast.
If not i would suggest asking on WordPress stackexchange, as you’re more likely to find some experts there:
https://wordpress.stackexchange.com