I see your issue but other than applying a body modifier to the Wall ("faking it"), as you did, I do not see a way around it. Applying the profile to the Door/Window Assembly does allow the Wall to infill in a 3D or elevation view, but apparently it does not fill in for a plan view. I have never had a situation with a transom-only light that extended beyond the width of the door, so I never encountered this before now. I had always had a partial height sidelight when using a profile to make a Wall "fill-in" under a Door/Window Assembl... that did not extend to the floor. The sidelight graphics filled in the "blank" space in a plan view.
Like you, I would have expected that if the "sidelight" was above the cut plane, that the Wall would show as Cut, unless the Hide Lines Below Openings Above Cut Plane toggle on the Other tab of the Wall Display Properties was checked. Perhaps the feature designers also expected that we would have a sidelight to show and the omission of the Wall under the transom is "by design". You may want to provide feedback to the development team on the Autodesk Product Feedback page.
David Koch
AutoCAD Architecture and Revit User
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