@KatieSteele What you're seeing is due to the versions of the ArcGIS API for JavaScript used in Web AppBuilder and ArcGIS Online's default MapViewer. Web AppBuilder was built with the older JS API version 3. The default MapViewer in ArcGIS Online - rolled out earlier this year - is built with the new JS API version 4. While both APIs use the same webmap specification, they have different ways of implementing popups, as your two pictures captured.
Work-arounds to consider:
Create your web application using Experience Builder, which is based on JS API 4.
Create a 3D web application in Web AppBuilder. 3D is built with JS API 4.
Customize your popup using Arcade and HTML.
Regards,
Rudy
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