Most people can't drive at all with both feet, or they drive less safe.
But once you are used to it, you drive MUCH safer, because you reaction time is MUCH shorter. Pilots (especially helicopter pilots) use both feet, too (albeit for steering, not acceleration). You just have to train it. Pilots learn it in no time - why not drivers?
The "overlapping" of "both inputs" usually happens when you shift from one-pedal braking (aka "slightly depressed accelerator pedal" that leads to recuperating) to wheel braking (depressed brake pedal). And it shouldn't be confusing to the board computer at all, on the contrary; it's actually very logic:
You are ALREADY decelerating via recuperation, and depressing the brake pedal is simply ADDING to the deceleration. Both inputs ("motor: recuperate" & "wheel brakes: also decelerate") should work flawlessly together - and in fact do in many EVs
Obviously it's different when the accelerator input doesn't lead to a recuperation (and hence deceleration), but instead to an ACCELERATION: in THAT case the dual input should really trigger a warning.