I found that pop-ups in apps created with the Swipe/Spyglass template do not allow the user to click through pop-up attributes for the overlapping polygons in the same layer; it only shows the top most polygon. Esri tech support referenced Enhancement Request: ENH-000097844 and recommended that I write this as an idea to show support for the enhancement. ENH-000097844 by the Product Team with the explanation of "We are looking at retiring the current stand-alone Swipe application in 2017 and adding a swipe widget directly to other story map apps. As we do this work, we will consider this request to show pop-ups for other layers." However the enhancement is not to show pop-ups of other layers but for overlapping polygons in the same layer.
The pop-ups in other web app builder templates like Simple Viewer allow users to click through attributes of overlapping tracts like the identity tool in ArcMap/ArcGIS Pro so I would assume that all pop-ups would behave the same regardless of the app template used. web map popups
