I think a lot of the stuff missing is similar to stuff released on the CD since many themes repeat throughout the show that correspond to certain characters like in a film score. But for me the one noticeably missing the most is the music from the orgy scene right after the intermission which features all the flame throwing and acrobatic stuff. There are a few places on CD that resonates with the music from that scene. But since it's one of the over the top and memorable moments in the show, the absence of piece in its full entirety on the CD was noticeable to me. There was another bit of music from the scene in the second half that I seem to remember wishing it was on the CD when I saw it the second time but those now dead brain cells didn't have a chance
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At the same time, I'm extremely grateful that we're getting an hours worth of original Stewart score on CD since most of his score releases are much shorter than that.