The tax regime is usually chosen when the company is set up, based on the margins and payroll of that moment. Years later the business is different and the choice remains.
Under Presumed Profit, the tax base is fixed regardless of the actual margin. Under Actual Profit, the company is taxed on real profit and takes PIS and Cofins credits. Companies with thin margins or heavy inputs often pay less under Actual Profit.
The switch can only be made at the start of the year, so the last quarter is the window to rerun the numbers.