This behavior occurs in XF 2.2 as well (though it is subtly different as the sidebar shares a scrolling context with the overall document). We could scroll the active item into view via JS when the page is loaded, but the end result is a bit jarring in its own way. Not sure if we'll action this.
If you have only XF installed, the navigation is ok. However, if you have installed several add-ons that make entries in the ACP navigation, it becomes a patience game.
If you scroll down to change something in phrases, for example, you have to scroll down 2 times. Really sucks!
Take the ACP navigation of IPB as an example. It is efficient.
Oh my bad, I thought that bug was more about Sticky-Kit behaving oddly. The video just shows the navigation jumping around unexpectedly when expanding a section or scrolling the document, without a page load.