It's surely a decision to present the cue as composed rather than the altered version used in the final edit.
Which, in my experience, is the normal practice for soundtrack albums. The whole point of them is to present the music in its pure form, in a way it couldn't be heard in the final film or episode. Using a version that's different from what's in the show isn't making a mistake, it's revealing something new.
Could it also have been a sound engineering issue? Perhaps at this point, they weren't able to dial out the sax as the track is now final? But back in the day, they were working with all the raw elements and could do what they wanted? I'm not sure how that works, but its a thought. It would be cool if FrontierTrek addressed this in the interview that's coming soon!
