Your reply is mostly correct and probably fine for a business in CA that only has one location and sells online to consumers in CA. Especially if that business does not yet have an established accounting method that involves destination taxes. But for many established business in CA, especially those with state-wide presence and sales forces, and an established accounting method of collecting destination taxes, this answer will not be acceptable to the accounting department and hence to the business.
Personally, I am a web designer who found that I had built just such an a 'solution'; for my client in Shopify. The site was finished and fully approved apart from taxes. I spent/wasted hours and hours following up with Shopify, checking in with the State (who are VERY clear that they accept taxes in two different ways, only one of which is offered by Shopify.
In the end, I did figure out a painful manual workaround, so that my site now charges destination-based taxes. I am putting it out here as this is probably the page that someone else loking for a solution will come to.
The fact that I can apply such a workaround, without custom code or Apps, proves that Shopify COULD offer us all the option to charge destination based taxes, if they only WOULD.
If you are a Plus customer, there are 2 switches that Shopify can set for you behind the scenes.
If you chose to establish Nexus in all states you CANNOT override the Product Sales Tax. You can, however, override the Tax on Shipping by adding a Nexus Value for that state. In our case the required Nexus in all states, always charge tax at the destination, and did not want to charge sales tax for Shipping in any state.
We had the 2 switches set and then added 1 ZipCode for each of the 31 US states to override Tax on Shipping to 0%.
@Abigail_Gorton Thank you for your post. I am chasing down this same trail and determined to resolve this for Shopify merchants as it is not just a problem in California. The problem I see with the workaround is that whenever California has rate changes for any of their 200 counties, you would need to update your tax overrides, which is again the same manual work having to be done again and again whenever rate changes occur.