Would it make a difference if I chopped the jalapeño after charring, but before I placed it in the container?

You could certainly slice the jalapenos after you cooked them, and before putting it in the containers to store. I would hesitate to slice them earlier, because that would change the rate at which they cooked through and absorbed the pickling solution. When I've made pickled jalapenos like this, that's what I do. Actually, I slice some and leave some whole- so everyone can pick how much they want, and that limits waste. You can also remove some of the seeds at the time, to control the heat level a bit.