Sony's Steve Berkowitz cast some light on the repair work that had to be done for the SACD remixes, in an interview published on the website of the now-defunct ICE magazine in August 2003. Regarding Blonde on Blonde, Berkowitz said,
"Here you have a four-track [master] tape that was done in two different places; you have a tape that's in rough shape, the oxide is falling off. We had to go through all kinds of means to patch things, from mono tapes to an eight-track cartridge master from original LPs, because there are literally parts of the oxide that you can see right through the tape."
In other words, where there was a dropout in the tape, they searched around for the best available mono or stereo source which wasn't damaged at that point and used that to patch in the missing content. I suspect that pasting from a mono or stereo source into a five-channel surround mix would be much harder to do without the joins showing.
(Thanks to ICE editor Pete Howard for this.)