The application does allow you to limit which autonumber masks display for particular users. To do so, navigate to System Setup | Autonumbering | Select a Mask Type | Add | Fill in the fields and select the Site ID. This will assign the mask to a user's specific Site ID.
You are also able to restrict which autonumber masks appear to users through System Setup. To configure the list of autonumber masks that display for specific user's sites, navigate to System Setup | User | Roles | "Display All Autonumber Masks" set from "On" to "Off".