The Geoprocessing widget in Web AppBuilder limits the user’s layer selection to only the visible layers.
In contrast, Experience Builder Analysis Widgets display all layers from the web map in the selection drop-down, even if they are turned off by default on the map. Our use case requires restricting the layers a user can interact with in the Web Tool widget. Please see the screenshots of WAB list (left) and ExB list (right).

It would be make for a better user experience if the tool would also limit the user’s layer selection to only the visible layers.