I view messages in their own window and do not use a message pane. So, in that window showing the message, I deemed the menu bar as the "message menu bar". Changes to the menu bar of this window are different from the main Thunderbird window. I did have to redo customizations to the main Thunderbird window, too.
For customizations I right click the menu bar, choose customize, then drag the little icons representing functionality where I want them to go. I put mark, next message, previous message, and delete on the menu bar.