Regarding the "missing" Spock's Brain cue just after "there is no mind" - it really looks like it was editorially created. It reuses the sting from "Poor Spock" and then segues into "Spock Walks." There's an overlay in there apparently, but there isn't a missing cue. It may have been reused in later episodes because they felt it sounded good and kept the edit for later use. Stranger things have happened.
Hmmm, I'm not sure. The "missing" cue seems to naturally fade, and sounds slightly different than the Spocks Walks cue, especially noticeable in, for example, the first few seconds of the scene in which Rayna plays pool in Requiem for Methuselah.