I solved the Apple Books problem with an automator script, using the "Copy to Clipboard" action. Then it can be assigned a shortcut in Keyboard preferences.
https://imgur.com/a/sG2isap
As you can see in that answer, I found a better method to assign the keyboard shortcut. Assigning the shortcut within App Shortcuts instead of Services lets you use the normal ⌘C shortcut in Books while not affecting copying in other apps.