Shopify does not have the facitly to differenciate products sold with or without VAT for the VAT Shipping charges.
It is a legal requirement to charge UK VAT for the Shipping when the product has got VAT viceversa if the product is a food product the shipping must not have VAT charges and unfortunately according to Shopify they don't have this function which causes a lot of problems with UK Customs and Bookeeping .
You are wasting your time trying to get Shopify to rectify the issues with taxation as these issues have been going on for many many years, Shopify just choose to stick their heads in the sand and pretend there's no problem.
Your only option is to leave Shopify for one of the other ecommerce companies some of them have a professional approach to having the correct tax implementation (Shopify do not)
I am from Zilverback, We built custom integration, automating your bookkeeping processes so you can focus on other things.
Our integration collects data from your payment gateways and booking your orders as paid to your accounting system. We can also custom integrate different VAT settings via account numbers facilitating it in your accounting system.
If you want to know more you can visit our site www.zilverback.com.