Aftermarket ECU’s allow you to tune out any performance or drivability issues that a stock ECU might not be flexible enough to address. You can change hardware like injectors or ignition system and simply make a change in the tune to support the new hardware. And aftermarket ECU’s provide engine protection features that keep the engine safe by shutting it off in case something goes wrong at wide open throttle, such as loss of fuel pressure, lean air/fuel, over boost, loss of crank signal, etc
You need a knowledgeable tuner to make it work. Or you need to get really interested in learning all about it and maybe take a few lumps along the way to do it yourself.