Did you ever sort out what to do with this issue? I am having a similar problem, where I would either like a "Deselect All" button or have the option to deselect all but one layer by default on launch while still keeping the other layers visible in the legend (turning off visibility on the Web Map fully removes them from the legend). As it stands, a user would have to manually deselect nearly a dozen overlapping layers on launch to start messing around with the map, which is really tedious.
