In many of the ArcGIS Online Template Web Applications the user can click through muliple pop ups at any point where there are overlapping layers. This option is not available in the template Swipe Application. Only the 2 layers involved in the Swipe have visible pop ups even if all layers had pop ups enabled in the corresponding Web map.
In the Swipe template Application the user should have the option to use the small arrow in the pop up box to click through muliple pop ups - just like the other template Applications.