I have seen infinite scroll paradigms that simply load the next bit of content, causing the page to elongate, causing the bar to shrink and reposition. This is fine to me as the bar remains in exact sync with the document.

I also think the scroll bar is an entirely desktop tool, and as infinite scrolling most benefits mobile, this is a moot point. Nobody on mobile uses the scroll bar.

Personally, as a middle-click-and-hold'er, I do not use the scroll bar. I just went through my pages and frankly I'm surprised how the bar looks. I honestly never look at it or use it.

As this article demonstrates the scrolling on mobile as well, I have to point out that your complaints are sadly more of edge cases w.r.t. to the products we're making for the general public.