Thank you for contacting us and I'll be happy to assist.
I couldn't reproduce this behavior on my test multisite environment.
Can you please share exact steps and also what error/warnings message is shown when you try to edit post relationships, as a super admin? A screenshot can further make it more clear.
Note: By design, The "Toolset" menu option is available inside the individual website's admin area, but not when super admin is inside the entire network's admin area.
( screenshot: hidden link )
Your understanding is correct and the super admin role has all the capabilities that an administrator role has and the relationship editor on the relevant post edit screen should be accessible.
While logged in as a super admin, can you visit the book edit screen again and check the "Screen Options" drawer at the top right corner?
If the checkbox for the "Book Authors" section is not checked, please check it and click the "Apply" button.
( screenshot: hidden link )