Usually packages don't modify code in core Emacs or in other packages. Often, they use package-supplied "hooks" to add behavior to other packages. Failing that,

Usually packages don't modify code in core Emacs or in other packages. Often, they use package-supplied "hooks" to add behavior to other packages. Failing that, there's the possibility of 'advising' functions to add/change behavior at certain points without actually monkeypatching. I've never seen a distributed package actually monkeypatch anything, though it is something you could do in your personal config.