Design Options - Structural - Referencing Errors

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I'm new at Design Options, and I have read through the online information from Autodesk about the feature, and I have experimented for a few hours with what I need to do, and I have come to believe that there is a big error in design options when it comes to structural models.
The referencing error keeps popping up and I understand what it means, but if I have 2 design options which include the foundation to roof, floor slabs in between with their supporting beams and walls and a few edge columns, and I want to "step back" a portion of the wall in my secondary option which would include stepping back the floor slab and the columns that support the floor slab, I cannot add the beams that support the slab to a design option because they are connected to columns on the opposite end that are not in the design option. It's a "chain" effect that is making me include beams and columns in 2,3,4 bays back that aren't part of my design option just because they're "connected". So unless modeling the beams incorrectly so they don't connect is the only answer, design options for structural use is very very limited. Any answers out there?
I have 2 images below, showing the "setback" design option I am looking to create and the "primary" or current design.