In our Company we actually have a main holding company and then the brands underneath. Each brand is in it self a separate Company so we find it give great flexibility. As we can report on usage and equipment by company.
There are several features that you can use if you set up your users to be in different companies:
1. Automatic routing
2. You can create categories which are unique to users from each company (so for example, you can create different category set for each department and not worry that users from other departments will use it)
User and asset licenses are not effected by the amount of companies/departments you have, if you have 400 user licenses, then you can place them in any company/department and this will not effect the licensing itself.