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.