The opacity of Treads does not influence the visibility of Tread Plates on the Floor Plan. The Structure of the Stair, if checked to be visible, will be displayed properly regardless of the opacity of Tread. So it is not the case of Treads overlapping Tread Plates in 2D.
I am not exactly sure but I think what happens here is that Structure GDL Objects (such as "Flight Beam 21") are not scripted in a way to be able display Tread Plates in 2D, only in 3D. So the Structure is displayed in 2D only in a simplistic way, mostly the bounding box geometry of the Beam/Cantilever/Stringer is displayed.
You should create a wish for option to display details of Structures (Tread Plates etc.) in the 2D of Stairs.
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