Questions like this, though, are easy enough to answer. The original GNP album presented that cue and Silver Orbs separately. They were recorded separately so that made sense
A lot of changes in the box set are made editorially to match original on screen usage. Whether one prefers that approach is another story and an individual preference.
Yes, this is correct - at least for Track 20. The cues as presented on the GNP release can be synchronized with the episode in question if edited to match; therefore, these cues were recorded separately. The new set edits Track 20, but the edit is not the same as in the episode. It is close, but not entirely accurate. It is not, as you might say, note for note spot-on correct for lack of a better phrase. The edit in the episode is cleaner and less noticeable. Here on the set the cresendo (I think it is called) at the end of the first cue overlaps the music in the second cue. It does not seem to match "as-is" any copy of the episode that I have to check as the timing is off on the edit. As you mention, the cues are different in the pilot version and I conclude that the syndicated version was used as a template.
And now, I must get to work -- have fun guys!