The version of the PDF annotation plugin that is being integrated into core will only be a feedback plugin, not a submission plugin. It will allow you to annotate PDFs that have been submitted via the 'file' submission type (or any other submission type that produces files, so, for example, a submission plugin that integrated with an external system for scanning to PDFs would be included in the files that could be annotated).
As a result, the submission features of the PDF annotation plugin will not be present - the main feature being the coversheet functionality.
I may look at creating a new 'coversheet' plugin to allow files to be uploaded by the teacher as a coversheet (and optionally, in the case of PDFs, filled in via a form on the student's submission page). However, the chances of me having some spare time to write this are slim, so it might be something that would happen if there was some funding available for it (it would almost certainly be an adaptation of my current PDF submission plugin).