I have a WEBAPP using a WEB MAP and a WEBAPP using SCENE. The layers are the same, with the Web Map based APP, I have the option to turn off and on labels, and more... with the SCENE based map I do not have this option.
I can edit the LAYER options in the Web Map based map but cannot in the Scene based Map. What is more confusing is some of my layers are labeled and others are not... There is no 3 dot options to adjust to manipulate the Layer like what shows up in the WEB MAP based WEBAPP
You will have to use Scene Viewer or Pro to make those edits to your web scene and not use WAB.