Hi @QuinnMChavez , You can set a web map with feature layers as a basemap in a map tour, and the feature layers will be visible, but the pop ups are disabled within the map tour. This is to avoid confusion and navigation issues between the map tour points and the basemap's features. If you want to see this as a feature down the line, I would recommend posting in the ArcGIS StoryMaps Ideas page requesting this enhancement.
Another option may be to create a sidecar that adds the web map, which can include the pop ups. You could then add media actions in the narrative panel to zoom to certain parts of the map, or open a new map; you could configure a second web map to add here that included both the "basemap" with pop ups and the new points within it. This workaround would take a bit more configuration, but could give you a similar effect to the map tour layout and navigation!
--Abby
