They're a problem on non-mobile, as well. If the bar is over content, but the scrollbar isn't adjusted for it, pressing space or pagedown doesn't move down one page worth of visible content. I don't get why breaking pagedown is acceptable. It's my preferred way to read long text.
But I'm not sure exactly what the mechanism is that causes this; I thought it was simple a case of forgetting to add top padding to the page body, but that doesn't always seem to be the case. Last time I saw a site that did this, it already had the padding but still misbehaved in Chrome. Yet the paging worked correctly in Firefox! Further testing showed Safari worked, so (in this case, at least) it seemed to be webkit-related.
But that's just one scenario. I suspect there's a number of ways people get this wrong, and it's unfortunately not just a single simple fix for all cases.