I've added my comments to the thread you mentioned,
over here.
It does seem to be the Kindle's fault. If the PDF viewer didn't mutilate high-quality images as it displays them (it displays them just fine using the MOBI display engine), then we'd be home free. Sadly, until they improve PDF support, there's no elegant solution that combines full-screen, high quality page views and the ability to navigate/jump to page/bookmark, as the Kindle's CBZ or image viewing support is severely lacking for the reasons mentioned in the
beginning of this thread.