We are also located in CA and dealing with this same issue - and it's becoming more pressing, now that the Holiday season is approaching. Have you figured out a work-around, or has Shopify offered any suggestion? It seems hard to believe that this isn't a more common issue.
I haven't received any new suggestions yet. I agree, it's hard to believe it isn't a more common issue. It would be ideal if there was a field to enter the taxable amount. I can't imagine it's just CA.. For now, I'm just following the guidance from the state.
We're having this issue as well. We're bundling together products which consist of taxable/non-taxable services & products related to wedding. (i.e. a wedding photographer & DJ package that is one product, but the DJ is non-taxable & the photography is taxable). We're located in MN.