Everytime I add a new layer to my webmap that is used as the data source for my bookmark widget, I have to go through all of the existing bookmarks and turn of the visibility for the layers I just added. This is not a good practice for long term maintenance as the layers in a webmap may change frequently if they are used for multiple experiences. Presumably you create the bookmark when you have the appropriate layers already in the webmap, so it doesn't make sense to have new layers be visible by default.
The default should be that when a layer is added to the webmap it is not visible in the existing bookmarks.
