OK, I decided to Try It And See by making two trivial apps, one that hooked into and extended the other. Thankfully, my assumption was wrong.
So, for future reference:
Have the app you wish to hook installed on your dev instance.
Make the Class Hook in the usual way per the ACP, extending the other app's class
Develop and download your app as usual. You can install this app on systems that don't have the class you want to extend without making the installer complain. Useful!
Thanks for the help.