So in the EA Console > Groups (right click) Properties > Custom Ini
In this setting you have to create a custom ini using the commands below. You can only include 1 custom ini at a time, then save it and apply to the group, then you can do the 2nd ini. I've provided a screenshot of where to do this.
Unfortunately you can't disable the initial pop up after before installation since you can't provide custom ini changes prior to the deployment of the client.
I hope this helps.