Honestly, I don't understand why there is so much confusion going on here. You guys don't question your CA at all?
It is a simple rule, Get your turnover done computed as per ICAI guidelines. Where this turnover is less than the 44AB limit (Rs 2cr from FY 2016-17), the net profit has to exceed 8% of this turnover to avoid audit (there is another condition that overall income needs to exceed the basic exemption limit). This 8% profit is assumed to include all the deductions including depreciation.
With regards GP vs NP discussion, Income-tax just tax profits computed as per the provisions of the Act. GP/NP are just accounting jargons. It doesn't tax the net profit as reflected in the Profit and Loss Sheet, it taxes the profit as per BP sheet.