Most organizations have horribly convoluted organizational structures and processes, and SAP has been shaped by those customers over the years to cater to those clusterfucks.
A clean, sensible ERP system can only work if the organization it serves is also sensibly organized. It is much easier (and less risky) for a company to choose an ERP system that caters to them, warts and all, rather than overhaul the way it conducts business.
As the old saying goes, SAP and its customers deserves each other.