The supermarket is easy. Turnover is turnover. Before you work out profit or loss you have to know what your turnover is /was and it is all recorded on the statutory trading record. How you make your profit, high or low margins isn't of concern nor are any of the other before tax deductions. Tax on turnover is the first expense on the Balance Sheet. The rest like depreciation etc. are acounting tools to assess return on investment and other decision making tools together with what an enterprise is worth. Once again purely for investment purposes not tax.
Obviuosly the tax has to suit the operation being taxed.
If the GST can work in the case of high profit with low turnover why can't this. I would need an example for me to get my head around it however.