Jack, I think you've stated for yourself the reason that this Index has drawn some criticism. By it's name it purports to be an index of backbone speed or backbone congestion or a combination of the above. Not only is it not really an index of these items, it could further be argued that there's not even any reliable way to draw conclusions about backbone performance from the Keynote measurements. As you say, there are many other variables. So why not give this thing a name that reflects it's real identity as an end-to-end test from the Keynote Perspective Agent locations to various WWW servers.
This assumes that you consider web server location and web server performance to NOT be a part of overall network performance. Our view steps back a bit from that. The majority of traffic would appear to be webcentric. From an end users perspective, what does a web site on a specific network look like and how does that compare to a web site on another network? There are ENDLESS variables contributing to that including intercity links, hub architecture, host hardware, host software, peering, connectivity points with other networks, transit agreements, type of routers, ATM switching (or not). All contribute. We think most people notice Internet performance (or lack thereof) while viewing world wide web pages.