I’ve never used AI to control ATC. Neither do I use the copilot function.
Let’s say you’re picking up a clearance from ATC on the ground. They give it to you, but as soon as you click the reply button in the ATC window, the squawk code gets set automatically. Same thing if you are given a squawk code in the air. You could always set it before answering the ATC call, but that’s not how it’s supposed to be. Anyways, ATC will start prompting you if you don’t reply within a few seconds. In real life you reply to the ATC call first, THEN you set the squawk code. That’s how it should be in the sim too.
Unless I’m seriously missing something, I think we might be talking past each other.