tb1978,
The primary key for the permissions dataset is SiteId + ScopeId + RoleDefintion + LinkId. Permissions are granted by Scope so it is the ScopeId that is used as key and associated with the Web, List, Folder or Item. More at https://techcommunity.microsoft.com/t5/microsoft-graph-data-connect-for/mgdc-for-sharepoint-faq-what-is-in-the-permissions-dataset/ba-p/4075447
The UniqueId column is related specifically to items (Folders or Files), added to help with scenarios where you need the unique id of the item within the list. There are actually two of these: ListItemId (integer) and UniqueId (GUID). The complete hierarchy for Items is: TenantId (ptenant), SiteId, WebId, ListId, UniqueId (or ListItemId).
UniqueId is useful if you need to find the object in the Files dataset that matches a specific File permission (Permission to File). We do recommend using ScopeId if the content is finding the permissions matching a File (File to Permission).
You are correct that the schema definition is missing these. We are in the process of updating it.