In SSA ERP 5.0x this financial table you are referring to was only used for the budgetting and controlling modules. This table survived the BAANIV - BAANV upgrade, but only because it was initially forgotten.
The multi-company concept in SSA ERP LN is the same as in SSA ERP 5.0x.
Each type of department (purchase office, sales office, work center etc.) is linked to an enterprise unit. The enterprise unit has an operational company (logistic company) and a financial company. So the enterprise unit is the link between operational and financial company.