The board provides 5V to Pi, however, the shift register and ADC are powered from the 3.3V pin from Pi, because all Pi pins are only 3.3V tolerable. The other reason is that often these embedded Linux boards (especially BBB) requires external components to be powered strictly after the processor is powered, so using the 3.3V power derived from Pi (instead of 5V from OSPi) ensures this property.