Hi...as per my knowledge If you are powering from 3 cells, the nominal voltage is 4.5V. By the time they drop below 3.3V they will be dead.
I don't have the regulator spec, but it probably needs at least 3.5V input to keep the 3.3V happy. If the 3.3V rail does dip, the GPIO will still work but will find it harder to drive the outputs reliably. Other parts of the circuit may not be reliable either.
With a source below 4.75V, you can expect problems with HDMI and any attached USB peripherals.