I don't think the tools we use impact the user experience that much, certainly not as much as the designs we use or the UX choices we make. If a hybrid app has a bad user experience it'd probably still be a bad experience if it'd have been built as a native app instead.
The article calls out scrollbar hijacking. That is a very example of the tools screwing up the user experience.
You generally don't have those problems in native. Apple in particular designs their APIs to steer you in the right direction and make it painful for you to do something that goes against their UX guidelines.
