I have successfully saved a Site Template using the following PowerShell command:
Get-PnPProvisioningTemplate -Out $templateFile -PersistBrandingFiles -PersistPublishingFiles;
I'm looking in the directory that contains the Template. There is a subfolder that contains Default.aspx, but nothing else. The PersistBrandingFiles parameter should save off masterpages, sitelogo, alternate CSS and the files that make up the composed look will be saved, yet they are not there.
I find the documentation to be a bit sparse. I've searched extensively, but not many examples. Perhaps I'm completely missing something.