The content of the opf file is not directly editable through the plugin interface. This is by design. I'm not going to say this will never change, but that's the way it is right now.
The opf file is always rebuilt by the plugin interface to automatically incorporate all the changes to the various files that a plugin may have made.
Depending on what changes you need to make, there are workarounds to accomplish some things. For instance deleting a manifested file and recreating a new one (from saved data) will allow you to "rename" a manifested file.
EDIT: Scooped by 60 seconds!
