[link to original on tumblr]
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I examined the versions on the 30th anniversary edition of Odessey and Oracle from Big Beat. He's clearly present on the vocal-less backing track (more clearly in the right channel), but comparing that with the final version, I've discovered that they're actually two different takes. The tempi are different, which is the most obvious evidence, but also the piano part during the bridge is slightly different (despite Johansen's claim that it's harpsichord; it's actually tack piano).
But even in the final version, you can make out the slight change in instrumental coloration (again, more clearly in the right channel) when Atkinson comes in, at the same spot as he does in that other backing track - right before the second verse ("Saved you the room you used to stay in every Sunday…").
Johansen sort of makes a big deal of Atkinson's supposed absence on the track: "We also know from Paul Atkinson that his relationship was going through a particularly difficult patch at the time. Is that why he isn't present on the recording? Is this song, in fact, in vague symbolic form about the crisis he was going through?" Which is just ridiculous because he is present on the recording.