There are issues with just about every issue of Trek on video. The laserdiscs are not perfect because they were taken from the syndication masters. In syndication the opening/ending theme music was changed for a number of the early episodes that had the electronic sounding theme. Also, the original opening of The Man Trap with Gene Roddenberry's name in the opening credit (looking similar to Season 2) was changed along with the music. Some of William Shatner's opening VO's are not correct for the episodes. The VO was re-recorded a number of times over the course of the series, and often times they use a generic version instead of the episide specific version as that cuts the costs of doing multiple film transfers and restoration. As I recall, some epsiodes also lack "Also Starring" before Leonard Nimoy's name originally. The Desilu/Paramount logo is often slightly different at the end - sometimes with incorrect music or logos from other seasons, etc. Again, trivial to some but changes are changes...
Documenting all the changes over the years and comparing every version available is a huge undertaking and would require you to have very old copies of TOS as first syndicated by NBC (that still had the NBC logo intact at the end after the Desilu/Paramount logo) before the later late 70's changes were made. The problem is that most people may not have ever seen these early syndicated versions nor the original air copies -- and even if you have, you are going from memory from years ago unless you happen to have a copy.
As far as the cue sheets go -- I saw them for sale at a convention in the 70's. I should have bought them, but they were really very poor xerox copies bradded together... and I didn't realize I'd never see them again.
We will likely not see these from LA LA Land as you would instantly be able to notice music missing from their complete set. I also doubt that Jeff ever publishes a new book with more than 10 of the cue sheets -- and they are re-typed there so you still don't see the originals as apparently the cue sheets are considered legal documents which is why they can't be distributed as actual reproductions legally. However the data on these can be distributed if retyped... assuming someone has them? I have seen copies of William Shatner's contract around... someone must have them?