I always understood that the 16mm prints that were available throughout the '70s and early '80s (up until when the 1985 remastered tapes became available) were pretty representative of the originally aired episodes (any edits notwithstanding, which were usually crudely done by the local stations at their discretion). As far as studio alterations, we know the episode trailers for S1 & S2 were understandably changed for strip syndication, with the "Next Voyage" and Enterprise "Turn to Bridge" clip crudely superimposed over the original "Next Week" footage (and Nimoy's narration for The Menagerie Part 2 trailer had the word "week" crudely snipped from the line "You'll learn next week why returning Captain Pike..." As far as the audio tracks, aside from the WNMHGB opening titles and the Balance of Terror phaser effects, I also specifically recall the Enterprise flybys in S1 accompanied by an audible rumble but no rumble in S2 and S3. I personally didn't notice the change in the opening title theme in S1 back in the day (although strangely I did notice the difference between the S2 and S3 themes). With the 1985 remaster of course, the audio was significantly changed throughout the series, including the audible flybys, the torpedo effects in BoT, and the S1 title music. While I think there's written documentation of the theme music change in S1 from the original airing, the other changes are documented only by comparison to the syndication versions, correct?
My point is, in the absence of first hand evidence (documents, recordings, original broadcast prints, etc.) is it a Cushman-worthy stretch to assume that the pre-1985 syndication prints are basically faithful to the originally aired episodes? Given the state of the television business in terms of budgets and technology in the late '60s and early '70s when the syndication package was prepared, I don't see the studios going to the trouble to remix the audio for syndication (and as Maurice pointed out, the missing narration WNMHGB situation makes no sense; why remove it from just that episode?). I just don't think there's going to be enough evidence to show otherwise. In 1985 there was a business case for a thorough remastering (not the least of which was providing stations with professionally pre-edited versions of the episodes to allow for more commercial time) along with vastly improved transfer technology.