Short and much too simple answer is taxes; financial reporting; debt consolidation; reconciliation of common and preferred stock interests across the RRs; and clarification/resolution of the B&O controlling interest/ ownership of the WM.
The holding company provided a common vehicle for merging assets, liabilities, contracts, etc. under one legal umbrella. It also facilitated arguments for eliminating duplicative administrative functions, services, trackage, etc. across the three roads.
It was the tool for effecting the merger and cleaning up the loose ends resulting from said merger.