It depends on the system being used. A couple aftermarket units work really well. And the Coyote & Eco-boost has a ECU like you have never seen. It is WAY different than what you have tuned before. Especially with torque management. They also rely very heavily on the knock sensors to remove and add timing as needed. The system is a big departure from even the last generation ECU. Very complex but also very capable.They are a joke for removing timing.
They do work well for adding timing believe it or not.
I always disable them, because they give a false sense of 'security'
But seeing you are using a old system with a chip/flash stay away from detonation for sure. Steep learning curve with a boosted car. Hopefully you are nicer to your parts this next go around. lol Good luck