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Because they ARE different, and that pre-dates Google. If they treated them the same, they'd be breaking the standard.
[edited by: ColourOfSpring at 7:43 pm (utc) on Apr 6, 2013]
Seriously, anyone who has DNS control over a domain name - they're going to make two different sites - one www, one non-subdomain (non www) - two different sites? Technically they can do that, but it would be a marketing disaster. Who is going to say "www.foo.com" is our site that sells A, foo.com sells B". Nobody does that.
I don't think it's quite THAT simple. I've never actually submitted non-www version, it always appeared by itself.
I've had two clients who did that for dev purposes. Wasn't my choice, but it was already done when I got there. In each case the dev site was walled off from Google.
And if Google *did* treat them the same, then they'd get just as much flack for breaking the standard.
example.com | www.example.com - completely identical
m.example.com - same content but different pagination, layout