When I tell it to offset it doesn't change, maybe because it's a pony wall and not listed as a 'foundation'? So my only alignment options for the pony wall are exterior surface, interior surface, framing exterior etc...
I've always built split-levels on the first floor as a pony-wall 2x stud construction with 8" or 10" concrete as the lower half, then lowering the floor height as required.
From there I build the foundation and in the lowered split portion I tell the foundation to supply floor to rooms above and I raise the footing location to just below the slab (typically 4") This allows me to show the foundation on all the same level when I put it on a layout.
Perhaps there is a better way?