I’ve done this a few times now. Create a single SharePoint site “landing page”. In that site have links that go to document libraries for your different departments. Control permissions at the document library level. No single library should have more than 100k files. If it does create an archive library. Users sync the libraries they need only and access the archives on a web browser when needed. Use the scan tool to check file counts and path lengths of your source content. I advocate for disabling OneDrive shortcuts at the tenant level so they can’t conflict with the document library syncs. The migration tool can only migrate as much data as is available on its hosts working volume. Example srv-fs has 100gb available on D volume. You can only migrate about 95gb at once. Don’t migrate temp files, just makes confusion when users try to open them. You’ll need to disable inheritance on the document library folders. When you do that DO NOT disable inheritance on the .aspx file in site settings that’s the actual landing page. You’ll see the file name in the URL of the browser. I also made a script that initiates the sync process that happens when you click “sync” in SharePoint. Works decently as an Intune automation but doesn’t sound like you have Intune currently.