I understand that the tax breakdown in the Total Advance field in the invoice templates do not show tax breakdown by design when Tax included in Basic Rate is checked, but we are legally required to provide the breakdown in the total calculations. The government does not care how we set the prices, but the amount of VAT or other taxes like Excise must be broken down in the total calculations.
I hope users are actually given a choice in the behavior instead of just sticking to a single setting.