Reports such as https://en.wikipedia.org/w/index.php?title=Wikipedia:VisualEditor/Feedback&oldid=568123469#I_can.27t_edit_the_references suggest that the references list being present but not editable is causing confusion for editors.
It would therefore be helpful for VE to display a message (popup? tooltip?) whne the reference list is selected that explains how to edit references. The text of this message should be set on a MediaWiki namespace page.
I don't have a suggested default wording at present.