Add ‘&level=10’ to the end of the web app URL.
This fix the default extent and keep the layers visible when the application is reopened. The number 1 can be changed based on preferred default extent. The higher the number is, the more zoomed in the extent is. Here is the mortified URL of the application that is tested on:
http://ess.maps.arcgis.com/apps/webappviewer/index.html?id=a838983fcf50496db1d3734e042131da&level=15
This workaround does not fit the user's workflow because the application is accessed through the Featured content on the ArcGIS Online home page.