The only way to access the popups for a feature (that I am aware of) is using the identify method, which will only accept a screen point. I have a use case where I want to display a popup for features that are located within a polygon. The only way I can think of doing this is querying each feature layer, then using the centroid of the results to do an identify on the same feature layer. Is there a better way to do this?
Also it appears that identify only works on visible layers. In this case, the layers would not be visible.