We have dealt with this issue through our bundling app. Basically Shopify calculates the tax depending on your settings so as long as prices are set correctly for products the taxes should be calculated correctly. What is the problem you are having now with bundles of non taxable and taxable items?
Bundleup - bundle your products and unbundle your orders. MYOB Sync - connect your MYOB account to sync orders, customers, payments and inventory. Get in touch with our team here.
The main problem we face is that the 5 product build-a-box subscription is a static $30 however the items inside can be all taxable, all non-taxable or a combination of taxable & non-taxable. Checkout is unable to identify this and attribute the correct tax amount to each customers order based on their product selections.
As this is also a subscription service, a customer may decide to change their products month-to-month which may affect the tax that they should be charged.