Could you explain why the basement construction of the 2-story granny flat is so problematic?
A two-story granny flat (or two-story residential units of 80 sqm in general) is at least, regardless of its possible basement component, I’d say "atypical." Maybe we are partly talking past each other. You could roughly sketch to scale how one might imagine the building structure and its division into granny flat and later main house. So far, your words sound as if they imply a drawing already developed, which just hasn’t been presented here yet.