There have been a few comments made that they are not 100% broadcast accurate, but only largely in reference to sound effects.
Largely, that's the case, but there are a number of episodes that have weird music changes, added cues and such. However, for the most part, going by the DVDs or Blu-Rays should be good enough.
Just keep in mind that recreating a tracked episode is a huge undertaking if you want to be accurate. It took me days to do The Corbomite Maneuver and it wasn't until I was well into the editing that I realized how repetitive the music choices were. The same cue from Charlie X was used three times. And the Fesarius and Cube cues were reused over and over.
Another person is putting together Balance of Terror and the edits between the multiple episode scores to create one sequence are insane. If anyone gets all the episodes done, I'd be VERY surprised.