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.
1. [Common]
PopupDurationGreen=0
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.