JMich: Yes, the Script Extender may have to be written from scratch, but from what I recall, it was a different executable either way.
You see, main Denuvo function is to prevent modifications of executables and game code. And some mods like Script Extender is exactly doing the thing that Denuvo should prevent. At some point, modders might discover that Denuvo wont let them modify or extend scripts. For example, Script Extender never worked with cracked exe, pirates had to emulate disc image. And Denuvo is changing exe and libs, and also prevents them from being modified.
Conclusion: if there is Denuvo, modders might discover some very unpleasant surprises.