So after much back and forth with architectural and structural representatives here is the process we have come up to solve this issue.
1) Structural designer creates a model line and align/locks it to the center of the wall that has a thickened slab. Additionally they align and lock the ends to the walls where appropriate. This ensures that the model line stays centered in the wall if it moves and gets longer/shorter as needed as well. Last part, and rather important, make the line style "<INVISIBLE LINES>". This ensures the line doesn't show up in everyone elses project when the structural model is linked in.
2) The structural designer then creates a slab edge attached to the model line. We created a custom thickened slab profile that has the dimensions needed for structural engineers including variable thickness, width at the bottom of the footing, and slope of the edges.
3) Join the model line based thickened slab with the slab, and other slab edges providing a good cleanup.
This allows for accurate modeling, quantity takeoff, rebar coverage, etc. We just implimented this idea so we haven't fully vetted it, but the preliminary on-project testing looks good. Will update post if anything goes wrong.
Thank you all for your help and information.