According to this...
http://en.wikipedia.org/wiki/Magical_Mystery_Tour_%28film%29
It's footage originally shot for Dr. Strangelove. This is plausible considering the unused aerial shots from The Shining used for the "happy ending" version of Blade Runner. (There was an old story long since debunked that Strangelove footage was used in 2001.)
http://www.youtube.com/watch?v=BbKSr3vb32U
Someone should really do a fan edit where Deckard and Rachel end up at The Overlook. ;)
Since MMT came out the year before 2001, I think it's unlikely they got any footage from the cutting room floor. MMT was entirely shot on 16mm, and any discarded 2001 footage would have been 65mm.