Hi,
Already see the problem, it’s not possible to have the same word for several permalink settings.
In this case you have the “shop” in the Category, Product category and Product base.
It can be only used in 1 place, this is how WordPress works nothing with the theme.
It can’t assume several types because that way after the “shop” text in the url, WordPress would not been able to determine if the rest of the url is related to a product, a category or something else and point in the right place.
At the moment a left the shop only in the product basename just for you to check that it works on the product but not on the others.
-Rui