the documentation you refer to describes the specifics of the application level native scrolling feature. The view native scrolling mode is a different feature. In a nutshell, it uses an element with overflow: auto CSS property set.
Up to your questions:
1) - the native scrolling view still exposes a scroller object, mostly for compatibility reasons. You may use its scrollTo method. The problem you refer to sounds like an issue we have encountered on Android 4.0.* (or 4.1.*) devices. Please let me know if this is so.
2) The window.scrollTo approach is valid for the application level scroller, so I will not go into further details. The jumping issue sounds strange, though. Can you try to reproduce it in our Dojo
If you don't use those features, I would strongly recommend that you enable native scrolling for your views.
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