The Intercompany functionality was released in Navision 4.0 and since then remained the same. There is a real need for customers with multiple companies within one country OR within multiple countries to work with an integrated system. Although it is possible to use different Chart of Accounts structures, the user still needs to overide the mapped Intercompany account with the account of the subsidiary company.
EXAMPLE
Company A
G/L Account 40112 Intercompany Mapping is 40112 with 5100
Company B
G/L Account 5100 Intercompany Mapping is 5100 with 40112

Create an Intercompany Journal. Credit the account 40112 and debit ICP-B. Post transaction
Pick up the Intercompany Inbox Transaction: The account is now a Debit to 5100 and a credit to ICP-A
When accepting, the user need to type in change the account from 5100 to 40112 or else it is not possible to accept the transaction.

This effectively means that there is no integration within this module and most customers find it quicker to do the work manually than to use the Intercompany functionality.