Why don't invoices coming from the sync with Acuity (my online booking system) obey the "all invoices include GST" rule? I have to fix every single one manually.

I want to share a bit of information about your concern, jacintabull.

The invoices created from Acuity syncs in QuickBooks without taxes. The steps you have taken to manually edit the each invoice is the workaround. 

You'll want to reach out to the Acuity's Customer Care Team. This is to check if they have some options to include the taxes.

You can always get back to us if you have any additional questions about data sync in QuickBooks. Thanks.