I have a user that want's his web app to retain the same layers every time he opens the map, but is not concerned with where he left off as far as the map extent is concerned. He also does not want to click the popup box every time in WAB 2.0 as this is also a poorly designed solution. Is there any way to do this besides configuring the map in AGOL, I want to keep certain layers for general users.
Leo,
If you are not happy with the current popup that asks about restoring the apps state then your only option is to develop this to your liking. You can make changes to the code to automatically apply the last state . See this thread where I answered what code to change to make this happen: