Keep in mind that any changes you make in the configurator will not update any scenes you have already created. I would recommend just tinkering with the layer visibility within the scenes you have already created. I do this all the time, kick things off with stock ConDoc, then adjust layer visibility as needed.
Assuming you haven’t completely reworked the drawing set, the hatch should definitely be on the bottom of the stack. The only way it could show through like that is if the column 2D Graphic does not have a surface to block what’s below.
When troubleshooting I often go look at the individual scenes in SketchUp, then orbit around to better understand what’s showing. Another tactic is to make a copy of the drawing in LayOut, then ungroup and pull it apart. This way you can isolate the issue and check which scene is actually causing it. Just select the problem viewport and check the scene in the SketchUp Model inspector.
Let me know if this gets you any closer!