I would like for Pop-ups to be enabled by default for all layers within portal.
For example, if a user goes to the "Map" tab whithin portal and adds a map service layer, I want "Enable Pop-up" to be set by default. How can I accomplish this?
So not a full answer, but you could look at this option for working directly with the json configuration file. You may be able to script something to set the pop-up option to be enabled for all layers:
Automating Pop up configuration of web app in ArcGIS for Portal?