Unique to the live version of "Music from the Spheres" on Encore, "tremble" in the line "All around the world the people tremble" is sung with a melisma (G# G# A G# F#), musically giving a sense of the word's meaning. In the studio version, it's simply sung to two G#s.
Previously, I'd noticed (but apparently hadn't fully realized) that there's a brief quote of "Dies Irae," which is featured so prominently in "The Coming of Kohoutek." In the studio version, it occurs at ~4:10; in the live version on Encore, it's at ~5:27. It lasts only two measures (because it's so brief, I'm uncertain of the key for that section, but there's at least one sharp):
On both Nexus and Encore, "Music from the Spheres" is a few songs after "The Coming of Kohoutek," but this quotation links them in a small way and - along with the cosmic theme of each - provides a bit of cohesion.