Hi @Xaser3 ,
Thank you for reaching out and outlining your issue. Unfortunately, it is not possible to set a tax override at the variant level within Shopify, and as you mentioned in your post the tax override would apply to the entire product with all variants included. This is something that has been requested by a number of merchants and may be something we change in future, and I will be sure to submit your feedback to our development team.
My recommendation would be to list the larger sized items as seperate products, although I recognize this is not ideal. You can be up front with your customers as to why these larger-sized products cost more to avoid any confusion, either in your product descriptions or on an FAQ page on your website.
You could also try using a bundling app to improve the customer experience of viewing these products, so the regular-sized product with the VAT-exempt variants can be paired with the larger ones where VAT is charged. I’d recommend checking out some of the bundle apps on the Shopify App Store and seeing if this is something that works for you.