I think I understand what you're after. Assuming I'm correct, you've got the same setup we have, and the simple answer is "Yes, it works"
Let's try for some ASCII art of a directory tree:
Root
|--->Computers
|--->Special Accounts
|--->Accounts (*)
|-->Head Office Users
| |->Jim Smith
| |->Jane Jones
| |->Admin
|-->Sales Office Users
| |->Anne Blogs
|-->Remote Users
| |->Tom Blogs
|-->Groups
|->Admins
|->Normal Users
What I think you want is to have all of your users (head office, sales, remote etc) synced with Alfresco, and all the groups, but you want to avoid having accounts created for computers etc?
If so, set the sync to start at ou=Accounts,dc=root
(ldap.synchronization.userSearchBase and ldap.synchronization.groupSearchBase) and it should just work