It seems you are speaking on a hidden option MAIN_INCLUDE_ZERO_VAT_IN_REPORTS. Note that, like most hidden option, this feature may not be implemented everywhere.
After analysis of the goal of this option, it seems it should have no impact on the amount of VAT. It just hide or not lines with VAT = 0. So total of VAT and lines with VAT should be the same whatever is this value of this option.
Because the page report by vat rate goal is to show the amount of vat, we may not need to show the amount of vat when vat is zero but this may be interesting to see all for others. Best thing is to avoid to have to choice by a hidden option and instead have a "visible" filter criteria.
An idea for developer volunteers : A good implementation to have this option finished (so removed by becoming an official feature) may be to add checkbox "Hide lines with no VAT" in the filter banner. So we can use the dynamic choice of user to present or not the lines with no need of hidden option.