The relation between the scenarios is not changed when the system is extended but the impact in the Bio scenarios become somewhat lower, relatively speaking.
The major source of eutrophication is spreading of the organic fertiliser with emissions of ammonia and nitrate. The biogas engine and the biogas busses are also big polluters producing high emissions of nitrogen oxides. Incineration is the next in order, but is not affected much between the scenarios (except when landfilling). In the compensatory system diesel busses and production of virgin cardboard dominate the emission picture.
The following waste fractions are worth source separating: plastic, cardboard (small difference).