Isn't it the opposite?

Automated re-factoring means you can refactor duplicated code only as long as it is exactly duplicate.

Whereas the whole problem is that when somebody changes 3 out of 10 of the duplicate cases in a simple way that they are no longer exactly duplicate, and then somebody fixes a bug in one of the other 7/10 cases, they can update the bug across the 7 "duplicate" cases but they'll miss the 3 that aren't.

The problem with duplicate code is always when some of the instances get changed/fixed but not all of them. And that when somebody edits one instance, they often aren't even aware of all the other instances.

Abstractions are low-risk, because you know where the code is. If it's the wrong abstraction, you can fix that and know what you're fixing. Whereas with duplicated-yet-modified code, you've now lost the connections between them.