Are the original plans on file at city hall? Can you ask the previous owners what is what?

I think you have identified things correctly. I would plan the layout based on the location of the existing toilet and tub/shower drain (if that works); the location of the sink drain is not too critical as a 1-1/2" lavatory drain at 1/4" per foot slope can be run through a 3-1/2" studded wall horizontally for up to 6 feet. If the wall is made with 5-1/2" studs, a 2" drain can run 8 feet horizontally. The sink drain will require venting where the it drops below the concrete. I agree the layout/orientation of the pipes seems funky, oddly dimensioned and placed. I'm not scared by much, so I would not be averse to breaking up the concrete and relocating the toilet drain to a more logical location, one could do it in a weekend.