Nathan,
SQL licensing allows for 1 system dbase and any number of application databases except for another test copy.
I think you are asking about having a single application database with many companies versus having each company in a separate application dbase.
To be in the same application database, a company needs to share fiscal years, base currency IDs and acct/subaccts. Using a single app dbase also allows you to use the same vendors, customer, accts.
You can have intercompany transactions between different application databases but you have to run a process to export the data and then another process to import it. When the companies are in the same application database, the intercompany transactions are created when the batch is released.